Several hundred insurgent fighters in Somalia have reportedly defected to the government in the past week, following fierce fighting that began early this month between militant Islamist factions in the southern city of Kismayo. The split in the Islamist alliance could bring further turmoil and uncertainty to Somalia.

On October 1, two Somali Islamist groups, which had been close allies in the effort to topple the U.N.-backed Somali transitional government in Mogadishu, turned their guns on each other in the port city of Kismayo. Days of heavy fighting killed an unknown number of fighters and civilians.

Back to clan warfare

For more than a year, Kismayo, like several other key cities in southern and central Somalia, had been largely administered by a coalition of Islamist groups called Hizbul Islam and the al-Qaida-linked militant group, al-Shabab. But late last month, al-Shabab shattered that alliance by declaring a new administration in Kismayo that excluded Hizbul Islam members.

U.S.-based Somalia analyst Michael Weinstein says, on the surface, the dispute between Hizbul Islam and al-Shabab appears to be a straight-forward rivalry between the two Islamist groups, fighting for power in one of the most prized cities in Somalia. Taxes collected at the Kismayo port are a crucial source of revenue for both sides.

But Weinstein says he believes long-running clan rivalries, not religious rivalry, was the root cause of the conflict between the two Islamist groups.

"What I think is going on is a volatile realignment toward clan-based Islamist warlordism. I do not think it is between religious movements," he said.

Warlordism in historical perspective

Somali history shows that controlling Kismayo has been the goal of various clans that have historical claims to the city and its surrounding regions. But for much of the past decade, that power was in the hands of Barre Hirale, a factional leader of the Marehan, a sub-clan of one of the largest clans in Somalia, the Darod.

In 2006, Hirale and most of his Marehan militia were chased out of Kismayo by the Islamic Courts Union. With the support of neighboring Ethiopia, Hirale re-took Kismayo from the Islamists in 2007, only to be chased out again in August 2008 by Hizbul Islam and al-Shabab.

The two Hizbul Islam factions that captured Kismayo in 2008 - Ras Kamboni and Anole -- were Islamists fighting to turn Somalia into an Islamic state. But equally, they were members of Darod sub-clans that have long held a grudge against the locally dominant Marehan group.

Hawiye clan soldiers fight with Ethiopian troops in Mogadishu (2007 file photo)

Weinstein says Ras Kamboni and Anole saw an opportunity for their respective sub-clans to reclaim power through Hizbul Islam. But the rise of Ras Kamboni and Anole threatened Marehan clansmen and sub-clan members of Darod's biggest rival, the Hawiye, in Kismayo. They aligned themselves with al-Shabab, hoping their support of the extremist group would elevate their clans to positions of power as well.

Since the fall of Somalia's last functioning government in 1991, the country has been plagued by clan-driven civil wars. Somalia's Islamist movement originally emerged as a way of bringing order to the country through community-based Islamic courts.

Islamic Union Courts militiamen take part in training exercises on the outskirts of Mogadishu, 11 Dec 2008

In 2006, the Islamic Courts Union defeated a coalition of C.I.A.-funded factional leaders, seized Mogadishu and restored stability in much of the country. But it was ousted from power six months later by neighboring Ethiopia amid reports that radicals inside the courts were gaining power. The Islamists launched an insurgency and have been fighting for control of Somalia ever since.

Somali political analyst Ali Roble agrees that clan interests are again playing a pivotal role in creating conflicts. But he argues current conflicts are being fueled by the leadership of al-Shabab -- men Roble says are so thoroughly committed to advancing the global agenda of radical Islamic groups, they no longer see themselves as Somalis.