He has maintained his innocence in the matter but said Sunday, "I've become a distraction."
"My resignation is based upon my realization that my ability to properly represent the Washington Nationals has been compromised because of false allegations contained in the press," Bowden said in a statement. "I am disappointed by the media reports regarding investigations into any of my professional activities. There have been no charges made, and there has been no indication that parties have found any wrongdoing on my part.
"At the same time, while I have done nothing wrong, I place a greater value on the love, respect and best interests of my family, friends, the game of baseball -- that I've served lovingly and faithfully for close to 25 years -- and, the reputation and future of the Washington Nationals, which I'm proud to have been a part of since its inception in 2004."
Sports Illustrated, citing an unidentified baseball executive familiar with the investigation, reported on its Web site last week that the FBI is looking at Bowden's actions as far back as 1994, when he was GM of the Cincinnati Reds.
Bowden met last year with FBI investigators looking into an alleged scam involving skimming signing bonuses for prospects from the Dominican Republic.
Details of the investigation initially were reported by ESPN.com in July 2008.
Bowden is the only GM the Nationals have had since the franchise moved from Montreal to Washington before the 2005 season. He has overseen a team that went 81-81 in that debut season but has finished worse than .500 ever since.
Last season, the Nationals were a majors-worst 59-102.
Bowden's 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.
Bowden also drew unwanted off-the-field attention, including in 2006, when he was charged with driving under the influence after failing a field sobriety test while in Miami.
The Nationals didn't immediately plan to announce Bowden's replacement.
His announcement comes two days after Jose Rijo, a special assistant to Bowden, was fired by the Nationals.
It was at Rijo's Dominican academy that the Nationals organization was introduced to a player it first knew as Esmailyn "Smiley" Gonzalez. He is the Dominican prospect who received a $1.4 million signing bonus in 2006, when the Nationals thought they were signing a 16-year-old shortstop.
Nationals president Stan Kasten said last week that a Major League Baseball investigation determined Gonzalez was born in November 1985, not Sept. 21, 1989. It also was discovered his real name is Carlos David Alvarez Lugo, Kasten said.
Rijo was credited with spotting Gonzalez in the Dominican about two years before the Nationals signed him.
"We greatly respect and admire the decision made today by Jim Bowden," Kasten said in a statement. "He showed characteristic poise and maturity and demonstrated his selfless love for the game and the Washington Nationals.
"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. 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."
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