“We have taken Marka, we entered alongside the Somali government forces this morning,” said Colonel Ali Houmed, the spokesman for the African Union mission in Somalia (AMISOM).
“There was some fighting, but not so heavy, most of the Shebab had fled.”
The loss of Marka, some 70 kilometres (45 miles) south of the capital Mogadishu, is another major blow for the insurgents, who have been on the back foot for several months.
AU and Somali troops have made significant gains in recent months against Shebab, although the Islamists remain a major security threat. Ethiopian troops are also battling the militants from the south and west.
The loss of Marka leaves the Shebab with two major ports in southern Somalia — Barawe and the key rebel bastion of Kismayo — although an international naval blockade has already greatly squeezed maritime access there.
The Shebab abandoned their last fixed bases in Mogadishu a year ago, where they have since reverted to guerrilla tactics, claiming a series of suicide attacks and roadside bombs.