Gunmen reportedly opened fire from a car in a drive-by shooting in the centre of the city, before racing off.
"Sheikh Adan Madeer was shot and killed in central Mogadishu by gunmen," witness Abdisalan Mohamed told AFP. "The gunmen then fled and got away."
Madeer, who was chairman of the parliamentary finance committee, is the fifth Somali deputy to be killed since the start of the year.
There was no immediate claim of responsibility, but Somalia's Al-Qaeda-linked Shebab have carried out a series of attacks in the restive capital.
"He returned from a mosque near his house... When two gunmen shot him dead. Now we are preparing his burial," Madeer's relative Nur Mohamed said.
Police official Ilyas Ibrahim confirmed the killing.
Shebab fighters fled fixed positions in Mogadishu three years ago and have since lost most large towns to a 22,000-strong UN-backed African Union force, fighting alongside government soldiers.
But they still hold sway in vast swathes of the rural hinterland from which they regularly launch guerrilla raids.
Recent Shebab attacks in Somalia have targeted key areas of government and security forces in an apparent bid to discredit claims by the authorities and AU troops that they are winning the war.
In May, the Islamist insurgents also launched a similar attack against the national parliament.
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