A person familiar with discussions within the organization told The Associated Press of the decision Tuesday. The person didn't want to be identified because the Marlins have declined to say whether Gonzalez will return next year.
An announcement from the team was expected later Tuesday.
Gonzalez's job was considered in jeopardy because owner Jeffrey Loria was upset that the Marlins failed to make the playoffs, although they finished 12 games above .500 with the smallest payroll in baseball. Loria met with organization officials Monday in New York to discuss the status of Gonzalez and his coaching staff.
ESPN.com reported Saturday that Bobby Valentine, an analyst for the network and a former major league manager, talked with the Marlins about a job. On the final day of the season Sunday, Marlins president David Samson declined to say whether Gonzalez would return next year.
In February, Gonzalez received a contract extension through 2011, and he has been praised in the past by Loria and general manager Larry Beinfest. In Gonzalez's three seasons as manager, the Marlins have improved from 71 wins to 84 to 87.
This year they were widely projected to finish fourth or fifth in the NL East but instead finished second, six games behind Philadelphia. They were five games behind wild-card winner Colorado.
The Marlins had the third-best record in franchise history even though they outscored opponents by only six runs. They went 30-20 in one-run games.
Florida's final victory this season was the 242nd for Gonzalez, and he passed Jack McKeon for most wins by a manager in team history. He's one of only three managers to lead the Marlins to a winning season.