"Kismayo has fallen and not a single bullet was fired," an Islamist source in the capital Mogadishu told Reuters on Monday.
The Islamic militia moved into the city after Colonel Abdikadir Adan Shire, also known as Barre Hiraale, the leader of the Juba Valley Alliance, a clan-based militia that controlled the area, fled on Sunday, officials and witnesses in Kismayo said.
Barre Hiraale's hasty departure from the city followed a split within the alliance on how to respond to the advance of the Islamic Courts Union (ICU), which seized Mogadishu and other parts of southern Somalia earlier this year, Yusuf Mire Mahmud, his deputy said.
"I wanted to talk to the ICU, and he did not. He sent a delegation to Ethiopia and that was the final straw for me," Mahmud told Reuters.
Many of the fighters of the Juba Valley Alliance belong to the same clans as the advancing Islamist fighters, allowing the Islamic Courts Union to easily occupy the city within the space of a few hours, early on Monday morning.
Kismayo is the largest port in southern Somalia
Abdullahi Hashi Gullale, a local resident, said: "On Sunday evening, the Islamic militia entered the town. Hirale and his militiamen have emptied the township and fled Berhane area," about 40km southwest of Kismayo.
In the past few months, the Islamic Courts Union has expanded rapidly from beyond its base in Mogadishu to take over large areas of Somalia.
Their advance has been at the expense of Somalia's largely-powerless interim government which is backed by Ethiopia and recognized by the United Nations and most foreign governments.
The interim government was formed in 2004 in an attempt to end the civil war that has divided the country since rival regional commanders toppled Mohammad Siad Barre in 1991.
Abdirahman Dinari, the interim government's spokesman, said any attack on Kismayo would breach a ceasefire deal recently signed between the government and the Islamists in Khartoum.
"We're requesting that the international community pressurise the ICU to stop attacking," Dinari said from the government's temporary base in Baidoa, near the Ethiopian border.
Thousands of Kismayo's inhabitants, fearing heavy fighting between the Islamists and the Juba Valley Alliance, have fled to Kenya in recent days, with 300-600 refugees arriving daily in the Dadaab camps just over the border, according to the UN.