In a letter presented to the speaker of the lower house, the lawmakers elected under Jonathan's Peoples Democratic Party (PDP) declared that they had joined the All Progressives Congress, stripping the PDP of its majority in 360-seat chamber.
They listed "divisions in the political party (PDP) that sponsored our election" as the reason for the move.
The PDP had controlled the lower house since the end of military rule in 1999, but was left with just 171 lawmakers after today's announcement.
Publicly, the president's rivals have said his political troubles are tied to poor job performance, but analysts argue the real divisions are linked to Nigeria's 2015 polls.
Jonathan is widely expected to seek re-election, but has faced mounting calls to stand aside.
He has been accused of breaking an unwritten rule in the PDP which calls for the presidency to rotate between Christians from the south, like Jonathan, and Muslims from the north.
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