The embattled administrator recently fought off an attempt to half the agency's $4 million budget over a controversy about paying a lobbyist.
Also, Kohler had been criticized by the head of SpaceX, Elon Musk, who complained that Kohler was trying to support a competing launch pad at Cape Canaveral.
"My capacity to serve effectively as president likewise has been damaged," Kohler wrote in a resignation letter to Lt. Gov. Jeff Kottkamp. "Therefore, in order to remove the unfair distraction and enable Space Florida to move forward with complete focus on space in Florida, I am resigning as president effective May 8, 2009."