The political shakeup, though, was unlikely to have much practical effect on Somalia's weak government, which controls only a few blocks of the capital and comes under near-daily attack from al-Qaida-linked militants.
Omar Abdirashid Ali Sharmarke told reporters he was resigning while standing alongside President Sheik Sharif Sheik Ahmed, who thanked the prime minister for what he called a "courageous decision."
"After seeing that the political turmoil between me and the president has caused security vulnerability, I have decided to resign to save the nation and give a chance to others," the prime minister said.
The resignation comes amid a rift between Sharmarke and Ahmed over a new draft constitution.
The two have not gotten along for months, and a vote of confidence on the prime minister had been scheduled over the weekend, though it was postponed. The two have a history of conflict: the president fired Sharmarke in May but quickly retracted the dismissal.
Ahmed called Sharmarke's decision "historic" because the impasse was settled among Somalis instead of seeking outside intervention.
Sharmarke, who holds a Canadian passport, became prime minister in February 2009 after the government signed a deal with opposition groups led by Ahmed.
The prime minister appeared far from downcast as he announced his resignation. Sharmarke smiled and waved to reporters as he left the news conference, which was well-attended by members of parliament and Cabinet members. The current Cabinet will lose their posts with Sharmarke's resignation; the next prime minister will name a new Cabinet.
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