State radio confirmed Mohamed's appointment on Thursday, quoting President Abdullahi Mohamed Formajo as saying the new mayor was the right choice for the role of accelerating the development of the city and the Banadir Region of which he is also governor.
Nicknamed Finnish, Mohammed becomes Mogadishu mayor a month after his predecessor Abdirahman Omar Osman died in an attack by a female suicide bomber, opening a path for him to lead a city, battles for which he fought and lost twice.
The former government minister, led a militia group that for almost a decade battled for control of territory in the capital in the late 1990s and early 2000s.
This was at the height of the instability in Somalia as disparate militias fought bitterly to fill the political void left after the fall of long-term ruler Siad Barrie.
He leads a splinter movement of the United Somali Congress which had initially professed loyalty to Ali Mahdi Mohammed during Somalia's then raging civil war.
After entering into a military alliance with Musa Sudi Yalahow as the latter's deputy, both men fell out and later engaged in a battle for Mogadishu.
He would join the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT).
The movement which was supported by the CIA battled the Islamic Courts Union but was routed by the Islamist militia in what is known in Somalia as the second battle for Mogadishu.
Prior to this Omar Finnish Mohamud Mohamed had momentarily shed his reputation as a warlord after being called to serve as Minister of Religious Affairs in a transitional government installed in 2004, a position he held until 2009.