The shootout, at a checkpoint in the Bakara Market area, involved fighters from militia that used to control it and gunmen loyal to the Islamic courts that took it away from them three months ago.
A clash at the same place last month killed two female passers-by.
The Islamic courts control most of northern Mogadishu and impose sharia law on its residents.
They took over the junction near the market, long a trouble spot in the lawless Somali capital, in September and have been manning checkpoints there ever since.