Kismayo was the last bastion controlled by al-Shabab, the radical Islamists allied to al-Qaida who taxed goods coming into the port to fund their activities. Al-Shabab announced their withdrawal from Kismayo, via Twitter, shortly after the Kenyan assault late last week.
But bitter clan rivalry is expected to hamper the creation of a new administration needed to run the city and port, say residents.
"We want peace, not clan feuds and a cause for al-Shabab's return," said Muhummed Abdi, an elder in Kismayo who spoke to The Associated Press by phone.
"We can share our resources and divvy it out peacefully without fighting," he said. "We should overcome disputes."
The clan rivalry centers on control of revenues from the port, which is one of Somalia's most lucrative business hubs.
Recognizing the threat of renewed clan fighting in Kismayo, the top U.S. official on Africa, Johnnie Carson, this week urged the Mogadishu government and the African Union forces to "go in very quickly and establish political stability and a political system that takes into account the various clan and sub-clan interests."
Kenya, the main military power that captured Kismayo, has invited the rival clans for a conference in Nairobi to establish an administration for the town.
"Life after Al-Shabab is really good and good, we don't see any more restrictions now," Sacdiya Hussein, a Kismayo resident said, referring to the strict Shariah law enforced by the rebels. "But during al-Shabab's reign there were not any clan rivalries, we hope it will remain so.
Kismayo's 2,070-foot-long (630 meter) four-berth port has long been the focus for bloody fighting, predominantly between the Marehan, Majerten and Ogaden clans.
However, Ahmed Aadi Aden, a Somali parliamentarian, warned that any clan rivalry for the control of the town would benefit al-Shabab and may provoke a resumption of clan wars from the years before al-Shabab, in which more than 700 militiamen were killed and hundreds more wounded.
"All forces in the town have participated in the town's liberation. They must be united for that cause," Aden said. "Their division will benefit al-Shabab."
The top U.N. representative to Somalia, Augustine Mahiga, said Thursday that Kismayo has one of the most complex clan mixes in Somalia and that the Somali people must work to achieve a sustained peace there.
"There are many clan dynamics that need to be understood, and I think this is high on the agenda of the new president and his incoming government," Mahiga said. "It may certainly be a very challenging exercise, but we have seen it happen in other recovery areas like Baidoa," he said, referring to another town al-Shabab once controlled.
Al-Shabab has been steadily marginalized in Somalia since it was forced out of Mogadishu in August 2011. Since then its taxes on goods coming into Kismayo port were al-Shabab's last major funding source.
As it no longer holds any major cities in Somalia, the extremists are expected to operate more as an insurgent force that carries out suicide and roadside bomb attacks.
The challenge is now on the weak Mogadishu government, and the allied African Union forces, to establish stable control over Kismayo.
"The situation of Kismayo has always been a difficult one and the clan rivalry will be further exacerbated by alleged siding by foreign troops with one of the clans in the city," Mohamed Sheikh Abdi, a Somali political analyst says. "Only an inclusive administration will dictate the future of Kismayo. Also if Kenya, with its history with Somalis, does not leave, I think they will just add more fuel to the fire already raging Kismayo" he said.
Al-Shabab found little popular support in Kismayo, say residents, because of the conservative brand of Islam it imposed on residents. Al-Shabab carried out public executions, whippings and amputations as punishments. The militants also enforced a conservative dress code and social rules.
"Somali forces are now patrolling the city streets. It's a big day and the end of the fear for us," resident Muse Ali said. "We hope the change will lead us into peace and clan agreements."