The biggest story out of Africa last year did not occupy the headlines the way dramatic revolutions in the Maghreb, civil strife in West Africa, the independence of South Sudan, famine in the Horn of Africa, piracy off the Somali coast, fraud-ridden elections in the ironically-named Democratic Republic of the Congo, and various other developments each did in turn.

Rather, as The Economist noted last month: “Over the past decade six of the world’s ten fastest-growing [economies] were African. In eight of the past ten years, Africa has grown faster than East Asia, including Japan. Even allowing for the knock-on effect of the northern hemisphere’s slowdown, the IMF expects Africa to grow by 6 percent this year and nearly 6 percent in 2012, about the same as Asia.”

Higher prices for commodities were responsible for part of the growth spurt, but other factors were also involved, including wise choices made by African leaders and peoples regarding economic reform, the rule of law, as well as the use of new technologies—all of which encouraged significant investment in their economies. The signs of hope, however, are now threatened by the spread of violent extremism by Islamist groups along the Sahel belt across the continent and the increasing links between the militants.

Al-Qaeda’s franchise in North Africa, Al-Qaeda in the Islamic Maghreb (AQIM), has been an unintended beneficiary of the fall of Libya’s Muammar Gaddafi. Buoyed by the flow of arms and fighters out of Libya, the group has in recent months initiated skirmishes with government forces in Mauritania, Mali, and Niger. Last week, its fighters boldly attacked a military installation in the Kidal region of northeastern Mali that had just been constructed with funds from the European Union’s Special Program for Peace Security and Development and unveiled at the end of November during European Commissioner for Development Andris Pielbags’s visit to the country. AQIM and a new splinter group calling itself the “Movement for Unity and Jihad in West Africa” have also struck at the tourism and commercial sectors with a spate of kidnappings of Westerners, including in the last month the abduction of tourists in Timbuktu and an engineer and a technician at a cement factory near the northern Malian town of Gao.

More ominously, AQIM has also increased its linkages with the Polisario Front which contests Morocco’s title to its southern provinces. In late October, three aid workers—an Italian and two Spaniards—were seized by AQIM militants, aided by Polisario sympathizers, inside a camp administered by the separatists near the Algerian town of Tindouf. The connection comes as no surprise given that the large numbers of idle young fighters with no prospects in camps presents the terrorist group with a ready pool of potential recruits, both for its military operations as well as the criminal activities it is increasingly involved in.

Meanwhile, further south in Nigeria, the Boko Haram sect has proven to be more and more of a threat to the security of Africa’s most populous nation. In testimony at the end of November before the House Homeland Security Committee, I noted that the group, far from being destroyed after the bloody repression of its 2009 uprising, had undergone a dramatic transformation. The upgrade in its operational capabilities was witnessed by the vehicle-borne improvised explosive device (VBIED) attacks it launched against Nigeria Police Force and United Nations headquarters in Abuja last June and August, respectively.

The extent to which Boko Haram will go to provoke sectarian strife in the country was underscored by the more recent assaults it carried out against churches across Nigeria’s “Middle Belt,” beginning with the bombing of a Catholic church in the Abuja suburb of Madalla as the congregation exited Christmas Mass, leaving more than three dozen people dead and scores injured. On Monday, a Boko Haram spokesman issued an ultimatum to Christians living in Nigeria’s traditionally Muslim northern states to leave within three days or face further violence.

The group was also responsible for a New Year’s Eve bombing of a bar adjacent to a military cantonment in Abuja’s Asokoro district, home of the presidential compound and generally viewed as one of the capital’s most secure areas. This latest attack, like the earlier ones carried out by Boko Haram, seemed to have been designed to show that the militants can strike anywhere and that they can make the country ungovernable for President Goodluck Jonathan just months after he won what I observed at the time were probably the most legitimate polls the Nigerian people have had in decades. In response, the government has declared a state of emergency in parts of the country hit by the insurgency and closed the northeastern borders with Niger, Chad, and Cameroon.

In East Africa, al-Shabaab insurgents in Somalia are probably at their weakest point in years, thanks not only to their own strategic overreach and the consequences of the famine (which their policies exacerbated), but also the combined military pressure applied by the African Union Mission in Somalia (AMISOM) force in Mogadishu, the clumsier Kenyan Operation Linda Ncha (“Protect the Country”) in southern Somalia, and the Ethiopian seizure over the weekend of Beledweyne, a key transit and trade hub near the border. However, as I noted after my trip to the bombed-out Somali capital last month, it is too soon to count al-Shabaab out. In fact, just like it did after the massive Ethiopian intervention five years ago, the group may well be shifting back to asymmetric tactics like roadside bombings and suicide attacks. Furthermore, the group potentially can tap into a large and restive potential ethnic Somali population, both indigenous and refugees, within Kenya itself. 

Even more worrisome than the threat the various Islamist militant groups in Africa pose individually is the growing evidence of links between them and what the commander of the US Africa Command (AFRICOM) has characterized as a “significant threat.” Speaking to reporters in Washington in September, General Carter Ham noted that AQIM, Boko Haram, and al-Shabaab “have very explicitly and publicly voiced an intent to target Westerners and the US specifically,” adding “if left unaddressed, you could have a network that ranges from East Africa through the center” and into the Sahel. AQIM’s emir, Abu Musab Abdel Wadoud, a.k.a. Abdelmalek Droukdel, has boasted of weapons and training provided to Boko Haram, whose leader, Abubakar Shekau, has used the North African group’s media outlet to proclaim his adhesion to jihadist efforts globally. The man whom Nigerian officials hold responsible for the bombing of the UN building in Abuja, Mamman Nur, had previously been sheltered by al-Shabaab in Somalia. While there last month, I was briefed on two groups of Boko Haram operatives who had received training at camps as recently as three months ago. 

Although it is unlikely that any of the current batch of Islamist militants operating across the middle of the continent is remotely capable of presenting an existential threat to any African states, much less regional powers like Nigeria, Ethiopia, and Kenya, they are fully able to cause a great deal of mischief, especially in the coming months. Counterinsurgency campaigns are, at the very least, expensive affairs which divert resources from the investments in infrastructure, education, and health which Africa’s emerging economies need to make if they are to position themselves to take advantage of the current growth opportunities. In many cases, the understandable reliance by governments on security measures to combat the threat posed by violent extremists brings with it the risk not only of further alienating minorities and other marginalized segments of the population, but of undermining, however unintentionally, that the fragile institutions of democracy in Africa. Moreover, even if violence can be kept far from commercial centers, it will nonetheless have a dampening effect on the confidence of investors for a region whose potential many are just beginning to discover. 

J. Peter Pham is director of the Atlantic Council’s Michael S. Ansari Africa Center.