Somali militia who have been fighting alongside the Kenyans also moved in, raising fears that the second city in southern and central Somalia which the Shebab had run for four years could descend into chaos.
The Kenyans "arrived from the west of the city and are taking up positions," Aden Ismail, a local trader said.
At least two other witnesses confirmed to AFP by phone that Kenyan soldiers from the 17,000-strong African Union Mission in Somalia (AMISOM) had entered the city, after remaining on the outskirts for more than two days.
It was not clear if the Kenyans remained in the city at nightfall. Yet other witnesses said they had seen only Somali militia in town.
"The ones I saw were maybe around 120 armed militants in dark green khaki uniform. but the Kenyan troops are not with those I have seen so far," Abdirahman Said, a Kismayo resident said.
He said some of the fighters carried a flag reading "Ras Kamboni", the name of a militia group with whom the Kenyans have been working.
Mohamed Yare, another resident, said some of the militia "were walking in the streets but without allowing the population to approach them."
Dhuhulow Abdirahman, another resident, expressed concern about the presence of Ras Kamboni in the city.
"They are from one clan and other clans will protest if they take control of the port and the airport," he said.
Residents have reported the presence of clan militia opposed to Ras Kamboni on the streets of the port city even since the Shebab pulled out early Saturday.
Kismayo was the main target of an operation launched by the Kenyan military almost a year ago. Its troops have since been integrated into AMISOM, whose bid to stamp out the insurgency is also supported by Ethiopia in western regions.
Observers have said that reclaiming Kismayo would cut off the Shebab's supply lines, strip them of vital funding and spell the end of their ability to control large swathes of land in southern Somalia.
The power vacuum created by what the Islamists called their "tactical retreat" after initially vowing the Indian Ocean would turn red with AMISOM blood had left Kismayo exposed to chaos and looming shortages.
"The town is very quiet this morning and there is no fighting but we have concerns about the clan militia roaming the streets," Ali Mumin, a resident, said before the Kenyan troops moved in.
It was not immediately clear how many AMISOM troops were taking up position in Kismayo but residents had mixed feelings about the change.
Asha Mohamed Aden, a seller of second-hand clothing, said she had seen "heavily armed Kenyans" entering the city along with Somali officers.
"They are carrying a lot of weapons," she said.
"Some people are happy to welcome them because they were fed up with the misrule" of the Shebab Islamists," another resident Abdullahi Farey Hassan told AFP by telephone, adding that he himself had "reservations."
Since the retreat of the Shebab, who ruled Kismayo with an iron fist, unidentified gunmen have killed at least three civilians, including a traditional leader, according to residents interviewed by phone.
The group's pullouts from its other key bastions elsewhere in Somalia have heralded a return to guerrilla tactics, including suicide bomb attacks.
Newly elected Somali president Hassan Sheikh Mohamud praised AMISOM Monday for forcing the Shebab to vacate the city.
Somali government sources said the administration is working on plans to mediate between the clans who are arguing over the control of the town in order to facilitate an "all inclusive administration" and avoid further violence.
The Shebab used Kismayo as an export hub for the illegal charcoal trade and the port had been their de facto capital since they abandoned fixed positions in Mogadishu last year, also under increased military pressure from AMISOM.
The Shebab still control the town of Jowhar, some 500 kilometres (300 miles) north east of Kismayo and one small port town, Barawe, lying some 230 kilometres (140 miles) up the coast from Kismayo.
Kismayo had also been a symbol of the extreme form of sharia or Islamic law the Shebab want to impose across the country since 2008, when they stoned a teenage girl in public on charges of adultery.
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