Republican Senate Majority Leader Dean Skelos resigned his leadership position Monday and will be replaced by state Sen. John Flanagan, of Northport.

In the six-count criminal complaint, prosecutors say Skelos used his power and influence to extort money from a real estate and environmental company for his son, Adam. They are facing extortion, fraud and bribery charges.

Skelos has said that he is innocent of the charges.

Flanagan emerged as Skelos' replacement after a three-hour closed-door meeting of Senate Republicans. Sen. John DeFrancisco, who had also contended for the top position, was at Flanagan's side as he announced his victory.

"We come out of this unified," said Flanagan, a 29-year legislative veteran who had led the Senate education committee. "There is a lot of work that needs to get finished."

In the formal Senate vote, Flanagan was elected leader with 33 yes votes. The 63-member chamber has 32 Republicans; in a symbolic move, the chamber's Democrats nominated Sen. Andrea Stewart-Cousins to be leader.