The Venezuelan was dumped after the Marlins went 69-93 this past season, finishing last in the National League East division.
The club have not yet named a replacement no replacement for the 48-year-old, who was suspended by the club for five matches earlier this season after making comments praising Cuban leader Fidel Castro.
"After careful consideration following the disappointment of the 2012 season, we decided to dismiss Ozzie," said Larry Beinfest, the Marlins' president of baseball operations..
"Our managerial search begins immediately and our hope is that a new manager, along with roster improvements, will restore a winning culture."
On Twitter, Guillen said the firing left him with "my head held up high, real high."
"To the fans that support me and for those who are happy as well my love and respect to you," Guillen tweeted.
"In life there are worse things and I have experienced them. I have lived through bad moments and I will get through this with support."
Guillen's comments praising Castro in a magazine interview angered Cuban Americans, who make up a large segment of the Marlins' fan base.
The Venezuelan manager apologized repeatedly at a news conference for his remarks, then began serving a five-game suspension only five games into his stay with the team.
Guillen joined the Marlins after leaving his post as manager of the Chicago White Sox from 2004 through 2011 at the end of last season.
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