VIERA, Fla. — Jim Bowden resigned Sunday after four seasons as the Washington Nationals general manager, leaving under the cloud of a federal investigation into the skimming of signing bonuses given to Latin American prospects.

He has maintained his innocence in the matter, but said Sunday, "I've become a distraction."

"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, and that's the Washington Nationals and baseball," Bowden added.

Seated at a table with Nationals president Stan Kasten before a small contingent of reporters and team officials, Bowden read from a prepared statement, sometimes deviating from the script as he struggled to contain his emotions.

No replacement was immediately announced.

"We're not planning on missing a beat," Kasten said. "Our staff has a meeting tomorrow morning, first thing. I'm not going to have anything to say to you about next steps for a while — later in the week."

Bowden is the only GM the Nationals have had since the franchise moved from Montreal to Washington before the 2005 season, overseeing a team that went 81-81 in that debut season but has been below .500 ever since.

Last season, the Nationals were a majors-worst 59-102.

His tenure with the club was marked by such moves as the trade for Alfonso Soriano, the failure to re-sign Soriano, free-agent busts such as Paul Lo Duca and reclamation projects such as Dmitri Young.

"When I came here ... the single thing that stood out for me about why we needed someone with Jim's skill is that he's resourceful," Kasten said. "We needed someone that would look around every corner, look under every rock to find the pieces that we could put into place. Because of that, we have a foundation that looks very exciting for '09."

Bowden also drew unwanted off-field attention, including in 2006, when he was charged with driving under the influence after failing a field sobriety test while in Miami.

"Like anyone else, I have made mistakes in all areas of my personal and professional life, but I leave here with the true belief that I have done nothing intentionally to harm the Washington Nationals or Major League Baseball," Bowden said in a statement released by the team Sunday.

He met last year with FBI investigators looking into allegations of skimming of signing bonuses and it was reported last weekend by SI.com that Bowden's actions are being looked at as far back as 1994, when he was GM of the Cincinnati Reds.

"I am disappointed by the media reports regarding investigations into any of my professional activities," Bowden said in his statement. "There have been no charges made, and there has been no indication that parties have found any wrongdoing on my part."

Bowden's resignation came three days after Jose Rijo, a special assistant to Bowden, was fired by the Nationals.

That was fallout from a Major League Baseball investigation that determined a top baseball prospect from the Dominican Republic who received a $1.4 million signing bonus from the Nationals lied about his age and name.

"We all believe it is imperative that we honor the integrity of the game and that fans be able to concentrate their attention and affections on the game and players on the field," Kasten said in a team-issued statement. "Jim has maintained his innocence, but recognized that he had become a distraction, and with great grace determined to do what was best for the team and his players."

The 47-year-old Bowden joined the Nationals, who were then owned by Major League Baseball, as interim vice president and general manager in November 2004 after a stint as an ESPN commentator. The interim tag was removed by Kasten in June 2006 and Bowden was promoted to senior vice president and general manager on Feb. 28, 2008.

During Bowden's tenure, the Nationals drafted third baseman Ryan Zimmerman with the fourth overall pick in the 2005 first-year player draft and helped reinvigorate the team's moribund minor league system. Bowden engineered several notable trades, bringing outfielders Austin Kearns from Cincinnati, Wily Mo Pena from Boston, Lastings Milledge from the New York Mets, Elijah Dukes from Tampa Bay, and Scott Olsen and Josh Willingham from Florida.

At 31, Bowden became the youngest general manager of a major league franchise when he took the reins in Cincinnati in 1992. Three years later, the Reds reached the NL championship series.

He began his major league career in 1984 in the Pirates' media relations department and later moved to the New York Yankees' front office before joining the Reds in 1989.