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The port is some 70km (45 miles) south of Mogadishu, which the Islamists were forced to leave last year.
"There was some fighting, but not so heavy," said a spokesman for the African Union mission in Somalia, adding that most al-Shabab fighters had already left the port.
The advance comes a week after a new parliament was sworn in.
Merca is the third largest port in southern Somalia and the African Union says its seizure will help in the operation to take Kismayo - the biggest town still in al-Shabab