Africa File

The Africa File is an analysis and assessment of the Salafi-jihadi movement in Africa and related security and political dynamics. 

Notice: The Critical Threats Project frequently cites sources from foreign domains. All such links are identified with an asterisk (*) for the reader's awareness.

The Salafi-jihadi movement is strengthening across several regions of Africa and will grow more dangerous in 2020 if current trends continue. This comes as the US seeks to limit its presence on the continent and shift its focus toward great-power competition with China and Russia—even though this competition is playing out in Africa. US resources are also focused on managing extremely high tensions with Iran. These dynamics place the US and its allies at risk of strategic surprise from the growing African Salafi-jihadi threat, particularly if intelligence, military, and diplomatic assets decrease.

Americans have a false sense of security that the African Salafi-jihadi threat is local. Local Salafi-jihadi groups underpin the global movement. Their sanctuaries in remote areas and in failed or failing states allow them to train, experiment, and prepare to take their capabilities onto the global stage.

These dynamics are playing out in East Africa, where the Somalia-based al Qaeda affiliate al Shabaab killed three Americans on January 5 in its first attack on US forces in Kenya. Al Shabaab already poses a severe threat to Kenya—a regional economic hub with key industries, particularly tourism, that are vulnerable to terrorist attacks. But al Shabaab has also demonstrated its greater ambitions by reliably aligning itself with the goals and rhetoric of al Qaeda leadership and seeking capabilities that could someday allow it to execute an attack outside the Horn of Africa.

The Salafi-jihadi movement is similarly ascendant in West Africa, particularly in the western Sahel region that includes Mali, Niger, and Burkina Faso. Militants aligned with both an al Qaeda affiliate and the Islamic State are growing more lethal and may soon establish de facto control over a large swath of this region. The tactics that these groups use to overrun military bases could someday enable attacks in Western capitals.

The rapid deterioration of security in West Africa is happening as the US Department of Defense considers withdrawing most, if not all, US troops from the region. This reduction could include ceasing support for the French counterterrorism mission in the Sahel, shuttering a US drone base in Niger, and reducing intelligence assets dedicated to the region. A new strategy for countering the Salafi-jihadi movement is needed, but a blanket withdrawal—paired with losing our awareness of what is going on—is certainly not the solution to a complex and worsening threat.

The US foreign policy community’s pivot to great-power competition creates a false dichotomy: Geopolitical competition and the Salafi-jihadi threat are not separate challenges but deeply connected ones. The Libya conflict is internationalizing. Foreign support—and now, direct foreign participation—is a key driver of a war now at risk of descending into unprecedented violence. Such conflict and grievance are exactly the conditions that, time and again, allow the Salafi-jihadi movement to manifest and grow. The gains that Libyans, Americans, and many others won against the Islamic State and its ilk in Libya in recent years will soon vanish if this regional conflict continues to tear Libya apart.


Read Further On:

At A Glance

East Africa

North Africa

West Africa



At A Glance

Global counterterrorism efforts are rapidly receding as the global counter–Islamic State coalition contemplates its next steps after destroying the Islamic State’s territorial caliphate and the US shifts its strategic focus to competition with Iran, China, Russia, and North Korea. US forces in Iraq temporarily halted counter–Islamic State operations on January 5 following a US strike that killed Qassem Soleimani, the commander of the Iranian Islamic Revolutionary Guard Corps Quds Force. The uncertain future of US forces’ presence in Iraq follows a disruption in US counter–Islamic State operations in Syria in the fall of 2019. Indicators of the Islamic State’s return are apparent in both Iraq and Syria, however, as the group recovers from the death of its leader Abu Bakr al Baghdadi and other senior officials in late October. The US administration also seeks to withdraw American troops from Afghanistan and is reportedly close to a cease-fire deal with the Taliban.

Meanwhile, the Salafi-jihadi movement, including al Qaeda and Islamic State affiliates and allies, continues to make gains in Africa, including in areas in which previous counterterrorism efforts had significantly reduced Salafi-jihadi groups’ capabilities. The movement is positioned to take advantage of the expected general reduction in counterterrorism pressure to establish new support zones, consolidate old ones, increase attack capabilities, and expand to new areas of operations. The Salafi-jihadi movement is on the offensive in Burkina Faso, on the counteroffensive in Libya, and stalemated in Mali, Somalia, and Nigeria. However, conditions in these last three countries favor the Salafi-jihadi movement rather than its opponents in the coming year.

Libya’s civil war, reignited on a large scale in April, will continue to fuel the Salafi-jihadi comeback, possibly allowing the Islamic State or al Qaeda to regain some of the territory they controlled before major operations against them from 2016 to 2019. The Islamic State’s comeback in Libya is part of its global effort to reconstitute capabilities after military defeats, an effort that the group’s late leader, Baghdadi, sought to galvanize in a September audio message. Stalemates in Somalia and Mali rest on the continued efforts of international coalitions, support for which is eroding in both host and troop-contributing countries, and on local partners that have demonstrated their inability to govern effectively or establish legitimacy in their people’s eyes.

Amid these conditions, US Africa Command (AFRICOM) is shifting its prioritization from the counterterrorism mission to great-power competition, a move also intended to reduce risk after a 2017 attack killed four servicemen in Niger. US and European powers aim to turn over counterterrorism responsibilities to regional forces of limited effectiveness—such as the G5 Sahel, which is plagued by funding issues, and the African Union Mission in Somalia, which is beginning a scheduled drawdown. French exhortations in the wake of the death of 13 French commandos in Mali in late November may increase European support for the G5 Sahel in the near term. 

The Salafi-jihadi movement currently has four main centers of activity in Africa: Libya, Mali and its environs, the Horn of Africa, and the Lake Chad Basin. These epicenters are networked, allowing recruits, funding, and expertise to flow among them. The rise of the Salafi-jihadi movement in these and any other place is tied to the circumstances of Sunni Muslim populations. The movement takes root when Salafi-jihadi groups can forge ties to vulnerable populations facing existential crises such as civil war, communal violence, or state neglect or abuse. Local crises are the incubators for the Salafi-jihadi movement and can become the bases for future attacks against the US and its allies.



East Africa

Al Qaeda–affiliate al Shabaab conducted its first attack against US forces in Kenya, killing three Americans. The January 5 attack targeted Manda Bay Airfield and the adjoining Camp Simba, which houses US forces providing training to Kenyan and other regional troops. The base is located in Lamu County, a coastal Kenyan region that borders Somalia and includes parts of the Boni Forest, historically an al Shabaab haven.

The attack signals an inflection in al Shabaab’s ability to strike hard targets in Kenya. It likely required significant planning. Attackers using direct and indirect fire and possibly a vehicle-borne improvised explosive device (VBIED) penetrated the base’s perimeter before being repelled by American and Kenyan troops. The attack also damaged American aircraft. US AFRICOM East Africa Response Force deployed troops to reinforce Manda Bay.

Kenyan police also arrested three men on suspicion of terrorist activities for attempting to enter a British Army training camp in a county north of Nairobi on January 5, the same day as the Manda Bay attack. The men were unarmed but carrying camera equipment, indicating that they may have been surveilling the base for a future attack.

The Manda Bay attack is the latest in a surge of al Shabaab attacks targeting foreign forces in the Horn of Africa in line with al Qaeda’s overarching objectives. Al Shabaab warned in October that such operations would increase, citing an October attack on a base housing UN and African Union personnel in Somalia and September attacks on a US-Somali airbase and an Italian military convoy in Mogadishu.[i] Al Shabaab media, other al Qaeda affiliates, and al Qaeda’s General Command heavily the September 30 raid targeting the US-Somali airbase.

Al Shabaab’s claim for the Manda Bay attack also connected it to a broader al Qaeda campaign. The group claimed the attack as part of the “Jerusalem will never be Judaized” campaign, a designation it also used for a January 2019 attack in Nairobi, Kenya.[ii] Other al Qaeda affiliates have also claimed attacks under this campaign.[iii] Al Shabaab subsequently promoted the Manda Bay attack as a sign of American vulnerability and alleged that US forces would abandon their Kenyan partners as they did the Syrian Kurdish forces.[iv] This statement sought to contest the legitimacy of the Kenyan and American forces by accusing the Kenyan forces of committing human rights abuses and erroneously accusing AFRICOM of downplaying the number of casualties incurred at Manda Bay. Al Shabaab also threatened to attack tourists in Kenya.

The Manda Bay attack was likely not an overture to Iran following the January 3 killing of Iranian Islamic Revolutionary Guard Corps Quds Force commander Qassem Soleimani in Iraq as some have suggested. An al Shabaab spokesman stated directly that the Lamu attack was not related to Soleimani’s killing.

Al Shabaab has escalated attacks in the Kenyan-Somali border region in the past four months. Al Shabaab militants attacked a telecommunications mast in Garissa County on January 7—a tactic used to disrupt communications to facilitate other attacks. A subsequent shootout between militants and police killed four children. The uptick in attacks includes a December 6 raid on a passenger bus that killed 11 people, including seven police officers, in Wajir County. The group has also emphasized attacks targeting Kenyan Christians.[i]

Al Shabaab has simultaneously escalated its rate of spectacular attacks in Somalia, including the highest-casualty bombing in Mogadishu since October 2017. Such attacks are intended to delegitimize the Somali Federal Government (SFG) and stoke instability at both the national and local levels. Al Shabaab conducted a VBIED attack in Mogadishu on December 28 that killed at least 90 people and injured dozens. Al Shabaab offered condolences to victims and admitted responsibility for the attack, which it said targeted a Turkish-Somali military convoy.[ii] The group accused security personnel of using civilians as human shields and has subsequently released its own assessment of the attack to challenge the SFG’s official account.[iii]

The December 28 attack follows al Shabaab’s first effective attack on a hotel in Mogadishu since February 2019. The group besieged the SYL Hotel near the Somali presidential palace, killing five people. Al Shabaab also conducted a VBIED attack that killed four people at a security checkpoint near the presidential palace on January 8.

Outside the capital, al Shabaab conducted an attack that may have been intended to stoke unrest in a region preparing for fraught elections. The group conducted a VBIED attack near a hotel in Galkayo, the capital of the Galmudug region in north-central Somalia, on December 21. The attack struck a military convoy and may have been intended to kill a Somali general.

Forecast: Al Shabaab will attempt a spectacular attack in Kenya in the first half of 2020. The group will also sustain a campaign of bombings in Mogadishu and elsewhere as part of a broader campaign to disrupt the planned 2020 elections. (As of January 9, 2020)



North Africa

Libya’s civil war is becoming increasingly international and escalating toward violence on the scale of the 2011 uprising against longtime leader Muammar Qaddafi. Foreign involvement—notably Turkish, Russian, and Emirati—has intensified in recent weeks and months. A joint cease-fire call from the Turkish and Russian presidents signals an effort to cut a deal that will secure their interests, but it is unlikely to stop the fighting. This conflict will not have a clear victor and may devolve into grinding urban combat in Libya’s populous cities, doing great harm to civilians and setting conditions for rejuvenating the latent Salafi-jihadi threat.

The Libya conflict has two main axes. The Libyan National Army (LNA), led by Khalifa Haftar, controls the country’s east and has a presence in the south. The LNA’s primary backers are Egypt, the United Arab Emirates (UAE), Russia, and Saudi Arabia. The LNA launched an offensive to seize Tripoli, Libya’s capital, in April 2019. This offensive has stalled despite Emirati air support and the deployment of hundreds of Russian Wagner Group mercenaries.

The LNA’s opponent is the UN-recognized Libyan Government of National Accord (GNA) and associated militias, many from the northwestern city of Misrata. Turkey has provided drones and armored vehicles to support the GNA in Tripoli throughout 2019, helping to stall Haftar’s offensive.

Foreign actors are pursuing a broad range of interests inside Libya. Several Middle Eastern states are competing to shape the future of governance in the Muslim world, particularly the role of political Islam. This competition, typified by the election and subsequent removal of Muslim Brotherhood member Mohammed Morsi as Egypt’s president in 2012–13, pits Saudi Arabia, the UAE, and Egypt against Qatar and Turkey. Economic interests are also at stake in Libya; Turkey seeks to protect an agreement with the GNA on offshore drilling rights in the Eastern Mediterranean, for example. Russia is pursuing various that include acquiring military basing, renewing or establishing economic agreements, and strengthening regional alliances.

Turkey is deploying troops to Libya in an attempt to alter the balance of power and achieve a cease-fire. The Turkish Parliament authorized President Recep Tayyip Erdogan to deploy troops to Libya on January 2. Turkey began preparing to deploy advisers and technical experts, with officials emphasizing that the troops will serve a coordinating and advising role rather than entering combat. Turkey may have already begun transporting Syrian militia fighters to Libya, though a proliferation of altered videos online complicates assessing these militias’ presence or strength.

Erdogan and Russian President Vladimir Putin are attempting to broker a truce in Libya that will secure their interests in the country and prevent escalation that would harm Turkish-Russian relations in other areas. They called for a cease-fire by midnight on January 12 and urged belligerents to reenter negotiations. Erdogan and Putin met in Istanbul on January 8 for the ceremonial opening of the TurkStream pipeline, which will transport Russian natural gas to Europe via Turkey.

The Russo-Turkish initiative is overtaking a parallel European effort to resolve the conflict. Leaders and diplomats from Britain, Germany, France, and Italy have also sought to engage with Libyan parties while condemning foreign interference in the conflict. Italian Prime Minister Giuseppe Conte sought to convene Haftar and GNA Prime Minister Fayez al Serraj in Rome on January 8, but Serraj reportedly canceled his meeting with Conte after learning of Haftar’s prior meeting.

The level of violence is increasing in Libya. An airstrike by the LNA or an LNA backer struck cadets at a military academy in Tripoli on January 4, killing and wounding dozens. Carnage of this kind is unusual in Libya’s war and may signal a shift toward higher casualty attacks in civilian areas. This strike came two days after the Turkish Parliament’s troop deployment approval and may have been intended as either punishment or deterrence for the GNA and its allies.

Haftar’s forces are attempting to consolidate gains before the January 12 deadline and may continue fighting afterward. The LNA captured Sirte on the central Libyan coast on January 7 and has continued to advance westward toward Misrata, where the majority of GNA-aligned militias originate. The LNA also announced the extension of a no-fly zone to Maitiga, Tripoli’s only functioning airport, on January 8. The LNA’s advance toward Misrata may be intended to draw Misratan militias away from the Tripoli front line to allow the LNA to advance there. It is unclear how Russia and Turkey would enforce a cease-fire if fighting continues after January 12.

Conflict in Sirte may create conditions for Islamic State militants to return to the city. The movement of militants in and around the city has been reported intermittently since US-backed Libyan forces ousted the Islamic State from the city in 2016.

Forecast: The January 12 cease-fire declared by Turkey and Russia is unlikely to hold. The most likely case is a grinding stalemate in a configuration similar to the current front lines. It is possible but less likely that the LNA will claim an initial victory by luring Misratan forces away from Tripoli and securing defections among Tripoli-based militias. This outcome would set conditions for insurgency, likely very quickly. Either branch—the stalemate or the LNA advance—preserves and worsens the conditions that will allow Salafi-jihadi groups to strengthen. (As of January 9, 2020)




West Africa

Security is collapsing and Salafi-jihadi groups are growing more lethal in the western Sahel, particularly in northern and central Mali, northern Burkina Faso, and western Niger. Salafi-jihadi militants conducted a series of large-scale attacks on military bases in Mali and Niger in late 2019. Civilian casualties have spiked in Burkina Faso in early 2019, and a humanitarian crisis is also worsening rapidly in the country.

The al Qaeda in the Islamic Maghreb (AQIM) affiliate in the Sahel—Jama’a Nusrat al Islam wa al Muslimeen (JNIM)—is capitalizing on rising violence in northern Burkina Faso by promoting itself as the defender of local populations. JNIM claimed a December 26 attack on Burkinabe soldiers as an act of retaliation for an army patrol’s alleged killing of 17 Fulani people in Soum Province on December 24.  JNIM claimed that civilians sought the militants’ help, indicating that the group seeks to build legitimacy to support its overall effort to install its own form of governance in the area. Security force abuses are a of support for Salafi-jihadi groups in northern Burkina Faso.

The Islamic State in the Greater Sahara (ISGS) is increasing the lethality and brutality of its attacks while reaffirming its connection to Islamic State leadership. A December 24 ISGS attack was one of the deadliest in Burkina Faso’s history. Raids on a town and military base in Soum Province killed 35 civilians, mostly women, whom Salafi-jihadi militants rarely target in this way. The Islamic State’s West Africa Province claimed the attack as part of the Islamic State’s “revenge invasion” campaign, a multi-affiliate campaign launched in retaliation for the killing of the Islamic State’s leader and spokesman in October.  The December 24 attack, paired with a January 4 roadside bombing of a bus carrying students, have caused a dramatic spike in Burkinabe civilian casualties in recent weeks.

The December 24 ISGS attack follows recent devastating ISGS attacks on hard targets in Niger and Mali. ISGS conducted the deadliest attack ever on the Nigerien army on December 11, killing more than 70 soldiers at a remote base near the Malian border.

ISGS’s and JNIM’s strategies may be diverging in northern Burkina Faso, and JNIM’s emphasis on defending civilians may also be intended to distinguish it from ISGS. The two groups are competitors that also deconflict and at times coordinate. They are also reportedly vying for influence and recruits in central Mali.

Salafi-jihadi groups are attriting local governance by targeting community leaders in the border region of Mali, Niger, and Burkina Faso. Militants killed and kidnapped several religious and community leaders since late November in northeastern Mali and western Niger. Militants also attacked security forces escorting election officials in western Niger in late December.

Attacks on military bases continued in northern Mali. Likely JNIM militants fired rockets at a base used by UN, French, and Malian forces in northern Mali’s Kidal region on January 9. The assault wounded 20 people, including 18 Chadian peacekeepers. For more on recent high-casualty attacks on military positions in Mali, see the November 13 Africa File

Forecast: Salafi-jihadi groups will begin to establish governing institutions—such as courts—in the tri-border area in the next six months. ISGS’s attacks on civilians will drive greater popular support to JNIM, which will present itself as a more moderate alternative. (As of January 9, 2020)


[i] “JNIM claims killing 11 Burkinabe soldier sin retaliatory attack in Soum,” SITE Intelligence Group, available by subscription at

[ii] “IS claims suicide bombing, raid on Burkinabe military base in Soum,” SITE Intelligence Group, available by subscription at

[i] “Shabaab claims killing 4 Kenyan Christians in ambush on Mombasa-Lamu road,” SITE Intelligence Group, available by subscription at

[ii] “Accepting heavy civilian casualties, Shabaab takes responsibility for Mogadishu blast killing dozens,” SITE Intelligence Group, available by subscription at

[iii] “Shabaab alleges Somali government exaggerated number of civilian casualties, minimized military loses in Mogadishu blast,” SITE Intelligence Group, available by subscription at

[i] “Referencing recent attacks on Western “Crusaders,” Shabaab declares operations will escalate until Somalia “liberated,” SITE Intelligence Group, available by subscription at

[ii] “Shabaab claims raid on U.S. naval base in Kenya, provides photo documentation,” SITE Intelligence Group, available by subscription at

[iii] “Al-Qaeda releases inaugural issue of “One Ummah” Magazine,” SITE Intelligence Group, available by subscription at

[iv] “Shabaab portrays Manda Bay raid as demonstrating American vulnerability, warns U.S. will abandon Kenyan forces like Kurds in Syria,” SITE Intelligence Group, available by subscription at

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