In a surprising move, the 50-year-old Rodriguez handed in his resignation, and it was accepted by Marlins president of baseball operations Larry Beinfest.
Brandon Hyde, the team's bench coach, was named interim manager for Sunday's series finale with the Rays at Tropicana Field.
"This morning I offered my resignation to Larry Beinfest and the Marlins, and they accepted," Rodriguez said in a statement. "I am grateful for the opportunity the Marlins gave me to manage at this level. It was a very hard decision for me to make, with the positive way the organization is moving; a new ballpark next season and the young core of players that this team has.
"I can't say enough about the effort that this staff and these players have put into this season. I could tell that they continued to give 100-percent effort each and every day on the field. I wish this organization, staff and players nothing but success in their futures."
Late Sunday morning, the Marlins had a closed-door meeting for about 15 minutes. Afterward, Beinfest addressed the media and noted that the search immediately is under way for a manager. The team must go through "the process," meeting MLB standards for hiring.
There are indications the Marlins will name a manager for the rest of the season within 24 hours, and according to a source, Jack McKeon, who managed the team to the 2003 World Series championship, is the front-runner for the job and is expected to be introduced as the club's skipper before the Marlins' game against the Angels on Monday.
McKeon, 80, is a special advisor to owner Jeffrey Loria. He last managed in 2005.
"This kind of caught us a little off guard," Beinfest said. "I know there's been a lot of speculation and everything, but this wasn't something on Father's Day and my son's 13th birthday that I thought was going to be happening today. We need to work. But we do want to get somebody in here quickly, so we can at least have some calm in the dugout and move forward."
The Marlins carried a 32-39 record into Sunday's series finale with the Rays and are in the midst of one of the most stressful stretches in club history. They've dropped a season-high nine in a row, and are 1-17 in June. The freefall came after the team was 29-19 on May 26.
"We are going to move as quickly as possible to get somebody in there so that we can move ahead with the business of playing baseball and trying to win," Beinfest said. "Brandon will guide us today, and we'll get home tonight and I'll be working through the game with Jeffrey and [Marlins president] David [Samson] and have somebody as soon as possible."
Beinfest noted that Rodriguez approached the team about stepping aside. It was not initiated by the organization.
But Beinfest added that everyone in the organization is vulnerable.
"When you've been going the way we've been going, I think everything is on the table," he said. "I'm probably on the table, as well, and rightfully so. ... I know there has been a lot of speculation and everything."
Rodriguez, the first Puerto Rican-born manager in MLB history, replaced Gonzalez on June 23, 2010. He was named full-time manager on June 28 of last year, and his tenure didn't quite last one calendar year.
The Marlins finished 80-82 overall last year. With Rodriguez managing, they were 46-46. His overall record was 78-85.
Over the past three weeks, the string of losses began to take its toll on Rodriguez. The streak of losing 20 of 23 is the worst in franchise history since the club dropped 25 of 29 from Aug. 13-Sept. 12, 1998.
"I'd like to believe this is an aberration, the performance of this team, because three short weeks ago we were in a much different place," Beinfest said. "I think we're capable of performing much better than we have. I don't know if that was the aberration or this. I'd like to believe that we're a much better team."
Rodriguez's close friend, third-base coach Joe Espada, was not shocked by the decision.
"Not very surprised. I know Edwin very well," Espada said. "He takes his job very seriously. Every day he takes the field, he wants to win. Right now, he felt that he was not the right voice for the club. He's a good friend, a good baseball person. But I know at the end of the day, Edwin is going to be fine."
One of the youngest teams in the league, the Marlins dealt with an emotional situation when hitting coach John Mallee was dismissed on June 8, and replaced by Eduardo Perez.
The Marlins are trying to stick together at a time there is confusion as to who will be their next manager.
"I think as a player you can always be surprised in these situations," first baseman Gaby Sanchez said. "It's just one of those things where you just have to accept it and continue to play and continue to go out there and continue to work hard and continue to play hard. This happens in baseball. This isn't the first time I've gone through this, it's not the second. It's just one of those things you accept it and feel like he's making the decision for him and that's what it is."
Wes Helms, a veteran leader on the squad, said Rodriguez's resignation comes at a time when nothing seems to be going right for the club.
"It's surprising, I guess, but I think it's more shocking," Helms said. "Right now, nothing is going right for us. This is icing on the cake. Right now, it seems like it's all negative for the Marlins. That's the way it is right now. It's tough to swallow. Edwin was great for us."