Kismayo must be the most disputed city in Somalia. Just recently two militias, both claiming to be loyal to the government, fought over the control Kismayo. One of the militias are from Puntland while the other group are Marehan, the first group was chased out of the city. While both groups say they're loyal to the TFG, government officials decided to support the first group and claimed the city was attacked by Islamic Courts militias, which is a bit of stretch. The dispute is a clan based one, the government sent troops mainly from Puntland which agitated the Mareehan militias who also supported the government.
After the civil war, Kismayo was seen as a Darood city and Mogadishu a Hawiye city. As Darood and Hawiye further split into sub-clans, and internal fighting irrupted, more and more disputes emerged over Kismayo. The villages around Kismayo are mainly Ogaden, a sub-clan of Darood, so they claim the city. Harti , another clan-group within Darod from Puntland also claim ownership over Kismayo. Mareehan, another sub-clan of Darood, from the region of Gedo, claim the city too. In the past 15 years alliances were formed and broken, and the city captured and recaptured by different tribal militias.
Just before the Islamic Courts took the city in 2006, an alliance of Habar Gidir and Mareehan controlled the city. After the Islamic Courts were ousted by Ethiopian troops Puntland forces fighting alongside Ethiopian troops moved into the city, Puntland forces stayed in Kismayo while Ethiopians troops moved on to Mogadishu. Mareehan militia supported the government and their warlord leader Barre Hirale became the defense minister. For the past few months tensions have been rising in Kismayo between Puntland forces and Mareehan militias on who should control the city. Finally, Mareehan militia chased out Puntland forces just when the government was busy fighting militias in Mogadishu.
The president of Somalia was the former president of Puntland so there's a conflict of interest there. The government has sent an negotiators to the militias in Kismayo to handover the city back to Puntland forces and that seems to have failed. It seems the government and the Ethiopian troops are preparing for an attack on Kismayo though the militia is saying that they fully support the government.