Sheikh Ibrahim Ismail was viewed as the successor to Aboud Rogo Mohammed, a controversial preacher accused of links to Somalia's Shebab insurgents, who was himself assassinated in a drive-by shooting in August 2012.
Rogo's killing sparked days of deadly rioting in Mombasa, with protestors accusing security forces of carrying out the killing, claims they denied.
"They were five people in a vehicle when it was sprayed with bullets," a senior police officer said from the scene, adding that one passenger survived. The attack took place late yesterday.
Some bullet casings lay scattered around the car, suggesting that shots had been fired after the vehicle had stopped, while Ismail's bloodied body lay slumped on the backseat with his companions.
Like Rogo, Ismail preached at Mombasa's Masjid Musa mosque, which attracts some radical followers.
Rogo was on US and UN sanctions lists for allegedly supporting the Al-Qaeda linked Shebab, including through recruitment and fundraising.
Last month the Shebab launched a deadly assault on an upmarket Nairobi shopping mall, killing at least 67 people in a four-day bloodbath.
