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03/01/09 1:23 PM EST

Nats general manager Bowden resigns

Longtime baseball exec denies allegations of wrongdoing

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.

Bowden started the day by holding a team meeting in the locker room, which was silent the entire five minutes he talked. He said he was leaving the team because he didn't want to be a distraction. Bowden was emotional during the meeting.

"I wasn't shocked because of all the speculation that was swirling. You hope it was done for all the right reasons," right-hander Shawn Hill said. "I still don't know what to make of it yet. I don't know what's going to happen from here. Hopefully it will turn out for the best."

About 10 minutes later, 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 announced his departure and maintained that he is innocent of any wrongdoing.

"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.

"I have become a distraction. Unless you are Manny Ramirez, there is no place for distraction in baseball. I want to be able to turn the page and I want this franchise to be able to have everybody, from the media to the fans, focus on what the game is about. It's about players. It's about what happens on the field."

Bowden is the second person to leave the organization in less than a week. The team recently dismissed Jose Rijo, Bowden's special assistant. Rijo has been linked to Carlos Alvarez David Lugo, who previously called himself Esmailyn Gonzalez. The shortstop, who received a $1.4 million signing bonus from the Nationals in 2006, allegedly falsified his name and age. In Washington's 2008 media guide, Lugo is listed as 19, but is really 23. Major League Baseball's Department of Investigations is looking into the matter.

Bowden was with the Nationals from 2004-09. The team never finished over .500 during his tenure. Their best season was in 2005, when they went 81-81.

Bowden was always working on a limited budget on the Major League side, forcing him to take some chances. Last year, for example, he signed free agents Paul LoDuca, Johnny Estrada and Rob Mackowiak, and all three were released before the season ended.

However, Bowden was given the money to rebuild the farm system and did an admirable job by drafting players such as third baseman Ryan Zimmerman, outfielder Chris Marrero and right-hander Jordan Zimmermann.

Bowden showed a good heart by acquiring reclamation projects such as Dmitri Young and Elijah Dukes. Young rewarded Bowden by winning the National League Comeback Player of the Year Award in 2007.

Young was emotional when talking about the man who gave him a chance to return to baseball when no other GM gave him the time of day. After the 2006 season, a lot of people thought Young's career was over when he was sentenced to a year's probation for assaulting his girlfriend. Not Bowden.

"He is that type of guy to give you a chance," Young said. "Jim forgets what happened in the past. He allows you to play ball and gives you every opportunity in the world. That's what he did for me. I saw him do it for Pete Harnisch, Ronnie Gant ... the list goes on and on."

Bowden had his share of controversy besides the current investigation. In 2006, he acquired outfielder Austin Kearns, infielder Felipe Lopez and reliever Ryan Wagner for five players, including right-hander Gary Majewski and shortstop Royce Clayton. It turned out that Majewski had a sore shoulder, and the Reds filed a grievance, which would be dropped last year.

That same year, Bowden was arrested for driving under the influence of alcohol and not passing a sobriety test.

In May of 2008, Bowden announced to a radio station that Chad Cordero would be non-tendered after the season. Such announcements are typically not made until the offseason. Cordero, who was on the disabled list with a shoulder injury at the time, was upset about Bowden's gaffe. Cordero vowed never to return to Washington.

Kasten said it will be several days before someone is named to replace Bowden.

"Today, I just want to talk about Jim and all he accomplished," Kasten said. "I can tell you that we are not missing a beat. Our staff has a meeting tomorrow morning -- first thing. I'm not going to say anything to you about the next steps for a while. There is a reason for that. It would be unwise to speculate or guess what's going on. I have some things I'm working on and things I have to think about.

"I assure you, we will not be missing a beat. We have a really deep staff here."

Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.