Correspondents say Friday's capture of the port will be a major political boost to allies of Hussein Aideed, one of the country's main faction leaders, who lost control of the central town of Baidoa (also called Baydhabo) on Monday.
Kismaayo was captured by militamen from the Somali National Front, which is allied to Hussein Aideed.
More than 20 people were killed in the fighting over the port, witnesses said.
The SNF is reported to have the support of the government of neighbouring Eritrea.
Morgan's men ousted
Kismaayo, which is Somalia's third largest town, had been controlled by the faction leader, Muhammad Said Hirsi - known as General Morgan - for the past six years.
An SNF spokesman said the remaining members of his forces were seen fleeing towards the Kenyan border.
General Morgan's whereabouts is unknown.
Kismaayo is the port for the fertile Juba River valley, where most of Somalia's grain is grown.
Ethiopia, Eritrea involved
Ethiopia and Eritrea, which are themselves embroiled in a bloody territorial conflict, are said to be stepping up their support for opposing factions in Somalia.
There are reports that Eritrea sent a shipment of arms last month to Hussein Aideed, who also enjoys the support of Ethiopian rebels.
The Ethiopian government is reportedly backing anti-Aideed factions in Somalia.
General Aideed recently said Ethiopian tanks and heavy weapons were used by the rival Rahanwein Resistance Army when it captured Baidoa last weekend.
Meanwhile, reports from Mogadishu say one of Hussein Aideed's wives has arrived in the capital, saying she had escaped after being taken prisoner in Baidoa by the RRA.
But RRA officials said the woman, Fartun Farah Yayure, had been released with other prisoners on humanitarian grounds.
Country profiles
Somali warlord blames Ethiopia for defeat
(08 Jun 99 | Africa)
Heavy fighting in Somalia
(06 Jun 99 | Africa)
Mogadishu market clash
(29 Apr 99 | Africa)
Gunning for the money in Somalia
(06 Apr 99 | Africa)
New beat for Somalia
(18 Feb 99 | Africa)
SomaliNet
Somalia Online
Ethiopian Government
Eritrean Government
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