From MLB.com:

VIERA, Fla. — Jim Bowden resigned as general manager of the Nationals on Sunday morning. His replacement has not been named.

Though he was under fire for his possible, though denied, connection to the alleged skimming of bonuses of Latin American players, he has maintained his innocence.

In an emotional news conference, with team president Stan Kasten at his side and assistant general managers Bob Boone and Mike Rizzo in the background, Bowden said he is leaving the Nationals because he did not want to be a distraction to the club.

“I’m today resigning my position as the senior vice president, general manager of the Washington Nationals,” Bowden said. “It’s an emotional decision. It saddens me, but I feel it’s in the best interest of two of the things I love the most: That’s the Washington Nationals and baseball.

UPDATE (by Chad): Mark Sheldon has this tidbit

Former Reds GM Jim Bowden resigned from the Nationals this morning. I don’t think I’ve ever seen Marty Brennaman so giddy.

Heh.