While these groups are mostly occupied with domestic issues, their anti-Western rhetoric and targeting of foreigners pose a wider challenge. So too does growing evidence of ties between armed groups from the Sahel and East Africa and Nigeria, observers say.
The three main al-Qaeda-linked groups are Somalia's al-Shabab in the Horn of Africa; al-Qaeda in the Islamic Maghreb (AQIM) which is active across the Sahel; and Boko Haram, which has sharply increased its attacks in Nigeria since 2010.
"We do have enough evidence of some communication between Boko Haram and AQIM and affiliated groups," a Washington DC-based analyst focused on the Sahel said.
While both Boko Haram and AQIM had claimed support or training from al-Shabab, this had not been confirmed, he added.
General Carter Ham, head of US African command Africom, warned in September 2011 that the various Islamist groups had said they wanted to "more closely collaborate and synchronise their efforts" in training and operations.
"If left unaddressed, you could have a network that ranges from East Africa, through the centre and into the Sahel and Maghreb, and I think that would be very, very worrying."
The seizure of northern Mali by hard-line fundamentalists has also stoked fears abroad.
Long a base for AQIM, involved in drug trafficking and the kidnapping of westerners for ransom, the region is now in the hands of Islamists intent on installing sharia law, who have openly allied with the al-Qaeda franchise.
Former colonial power France has repeatedly raised concerns that the vast desert could become a new breeding ground for terrorism.
AQIM grew out of the Algerian Salafist Group for Preaching and Combat which linked with al-Qaeda in 2006.
"We pray to God that they will be a thorn in the side of the American and French crusaders and their allies," al-Qaeda's then number two and now leader Ayman al-Zawahiri said at the time.
In January a UN report said ties had been established between Boko Haram in Nigeria and AQIM, along with its splinter group, the Movement for Oneness and Jihad in West Africa (MUJAO) – and the fundamentalist fighters Ansar Dine (Defenders of Faith), who currently control Timbuktu in Mali.
Northern Mali lawmaker Abdou Sidibe has said "a good one hundred" Boko Haram fighters had been seen in Gao, which is controlled by MUJAO. They are believed to be attending a MUJAO-run training camp.
Deadly government offensive
In Nigeria, Boko Haram has dramatically stepped up attacks on churches, government installations and other targets since resurfacing in 2010 after being crushed in a deadly government offensive a year earlier.
The US state department, which last month designated three Boko Haram leaders as global terrorists, says the group has killed more than 1 000 people since the beginning of 2011.
Despite some evidence of links to other African jihadists, some observers insist the group has a narrow domestic focus in a region crippled by poverty.
Professor Kyari Mohammed of Modibbo Adama University in Yola, a specialist on Boko Haram, is sceptical of claims that the group has extensive foreign ties.
"It's a local insurgency, but they are aware of global events," he said.
Statements boasting of its foreign links were possibly a bid to raise its stature as a global, extremist movement, he argued.
The links between al-Shabab and west African terror groups are also disputed.
On Monday, Kenyan Prime Minister Raila Odinga expressed concern the al-Shabab "could link up with other terrorist groups like Boko Haram in Nigeria".
He was the day after masked gunmen killed 17 people in attacks on two churches, the worst such attack for a decade.
But the al-Shabab themselves have offered little public support for other Muslim fundamentalist groups, speaking instead of ties to the Yemen-based al-Qaeda in the Arabian Peninsula.
Nevertheless, some experts such as Ahmedou Ould Abadallah, creator of the Centre for Strategy and Security for the Sahel and Sahara, are convinced the ties run deeper.
"There are al-Shabab Somalians in the Sahel region and I am sure they have links with AQIM and Boko Haram. I have material proof," said Abadallah, a former UN representative for West Africa.
"It is a real danger. They all consider themselves fighters for Islam."
Shehu Sani, author of The Killings Fields: Religious Violence in Northern Nigeria, said he believed the various groups were "relating with each other even if they are not working together.
"If you link the Chadian rebels, Boko Haram, the Tuaregs in Niger and now the rebels in northern Mali, you can see on the horizon an arc of terror. It's not an axis of evil, it's an arc." – Sapa-AFP