Officials from the Juba Valley Alliance (JVA) which controlled the region around Somalia's third largest city until its capture by the Islamists on Monday, gathered in a field to surrender their weapons on Wednesday.
Yusuf Mire Mahmud, the former deputy leader of JVA, said he had handed over 18 "technicals", trucks mounted with heavy weapons, to the Islamists, and was putting his 300 fighters under their control.
"We gave everything to the courts unconditionally," he said, after overseeing the handover.
"The fighters and weapons will boost the Islamist presence here and serve the people."
Islamists to deploy more fighters
The Islamists tested the surrendered weapons in a nearby field and then said that the 300 fighters would help them to seal Somalia's border with Kenya, about 150km south of Kismayo.
"This is a good contribution that will help bring lasting peace"
Islamist spokesman in Kismayo
Ibrahim Shukri, a spokesman for the Islamists in Kismayo, said: "We have received the JVA fighters as well as their war machines.
"This is a good contribution that will help bring lasting peace to Kismayo.
"It is a blessing of Allah when people surrender weapons for the betterment of the Islamic people of Somalia."
The Islamists seized Kismayo without firing a shot after the leader of the JVA fled the city on Sunday.
Since capturing Mogadishu in June, the movement has rapidly expanded its control over south-central Somalia and now effectively surrounds the provincial town of Baidoa, where the country's weak interim government is based.
Its takeover of Kismayo was met with two days of protests. One of the demonstrations ended in violence when the Islamists shot into a crowd, killing a boy.
Kismayo is the largest port in southern Somalia
Tensions in Kismayo became inflamed when one Islamist fighter tore down the country's national flag to replace it with the movement's own banner.
Following the demonstrations, an overnight curfew was imposed and several protesters arrested.
But despite the troubles, the Islamists said that remaining JVA officials were free to stay in Kismayo as long as they did not interfere with security.
"They can stay on if they want, but there are no longer part of the administration here," Shukri said.
He added that the militiamen who handed over their weapons supported the Islamist movement and would be taken to a "rehabilitation" centre where they will be weaned off khat, a mild leafy stimulant.