The decision to put forth a second candidate was spurred by fears that the ruling military council may use Egypt's election committee to disqualify Islamist presidential hopefuls in order to make room for former regime officials to win.
The upcoming election, slated for the end of May, is the first presidential vote since the ouster of Hosni Mubarak after nearly 30 years in power. It is a crucial election for both the military and the Brotherhood, which are already sparring for power. The military wants to keep control of key security and economic portfolios until at least June, when a new president is announced, while the Brotherhood is pushing to name a new government first.
In a statement released late Saturday, the Brotherhood said they are putting forth party leader Mohammed Morsi as an alternate to Khairat el-Shater, the group's chief strategist and financier.
Any candidates have just one day before the deadline for submitting applications to run for president. They will have to get the backing of 30 lawmakers or 30,000 signatures by Sunday evening.
The Brotherhood, which emerged from last year's uprising as the most powerful party in Egypt when it won nearly half the seats in parliament, said in its statement that there appear to be efforts by Egypt's election committee to disqualify certain candidates from the race.
"There are attempts to create barriers for some candidates," the Brotherhood said, adding that there are those who want the former regime to return to power.
Others who have expressed interest in running for president are Mubarak's ex-deputy and longtime spy chief Omar Suleiman, his ex-prime minister Ahmed Shafiq, and his ex-foreign minister and former Arab League chief Amr Moussa.
"Because we are protecting the success of the revolution and all of its goals ... we have decided as the Brotherhood and its party to nominate Mohammed Morsi as our back up candidate for president," the statement said.
El-Shater was released from prison last month after serving five years on charges relating to his membership in the then-outlawed Brotherhood under Mubarak.
Egypt's last four presidents have hailed from within the top ranks of the military. An Islamist candidate would erode decades of military control and place its ruling generals under civilian oversight.
The Brotherhood said el-Shater faces no legal obstacles to running for president and that this issue was vetted clearly before announcing his candidacy.
The announcement comes just hours after an ultraconservative Islamist group put forward a fundamentalist cleric as its candidate after reports surfaced that ultraconservative hopeful, Hazem Abu Ismail, could be disqualified from running. Egypt's election commission said Saturday that his mother was a U.S. citizen.
Speaking to hundreds of supporters in a mosque Saturday, Abu Ismail said he has proof his mother was not a U.S. citizen and called the allegations a "plot" against him.
The Gamaa Islamiya, or Islamic Group, said it selected Safwat Hegazy, a prominent imam who preaches on television and who took part in last year's protests as a back-up to Abu Ismail.
Last month France barred Hegazy from entering the country for an Islamic conference along with a number of other high-profile Muslim clerics on the grounds that they "call for hatred and violence."
Gamaa Islamiya leader Abdel-Akher Hamad there is concern that the ruling military council, which took power after Mubarak's ouster, may even go after independent candidate Abdel-Moneim Abolfotoh, a reformist among Islamists.
"It is clear that there is some kind of agreement between the military council and the election committee before any Islamists even put forward their name to try and disqualify them one by one," Hamad said. "We will not wait to be slaughtered to wish we had acted."