Musician Jimmy Buffett and actor Bill Murray have been minority part-owners of the team since . The majority owner is Marvin Goldklang who also owns a stake in five other minor league baseball teams throughout the country (Sioux Falls Canaries, Hudson Valley Renegades, Charleston RiverDogs, Brockton Rox, and St. Paul Saints). Murray is also a minority part-owner of the Saints.
In , there was a restructuring of the classification system of all Minor League Baseball, which resulted in the FSL changing from Class D to its current status of Class A-Advanced. They became a Baltimore Orioles affiliate in , and were renamed the Miami Orioles after their MLB parent club from –.
Upon the Baltimore Orioles' severing of their affiliation with the Miami Orioles following the 1981 season, the franchise reverted back to the Marlins name, and actually participated in the FSL season as an independent entry. Without a Major League Baseball affiliate, this team was composed of undrafted players from the area, free agents from various organizations and players on loan from the Baltimore Orioles, San Diego Padres, and Oakland A's organizations.
The following season the Miami Marlins became a San Diego Padres affiliate. This partnership only lasted two years, and the Marlins found themselves again without a parent club for the season. Again, they filled their roster with talent on loan from various organizations, along with eleven former major leaguers looking to rejuvenate their careers. They stuck with this formula through the season.
In , the Marlins were renamed the Miami Miracle after a group of investors that included Bill Murray and Jimmy Buffett purchased the club. They moved the team from Bobby Maduro Miami Stadium to Florida International University's University Park (the vast majority of their time in Miami, the team played at Miami Stadium).
The Miracle were sold again a year later to the Marvin Goldklang Group. Mike Veeck (son of Hall of Fame inductee Bill Veeck, and author of the book, Fun is Good) also became part owner of the organization while Murray and Buffett still maintained their shares as well. In , these new owners returned the Miracle to Fort Myers where it has remained ever since. The Miracle operated as a co-op club with the Minnesota Twins that season, and became a full Twins affiliate a year later. This Player Development Contract runs through 2012.
The Miracle captured the Florida State League First-half West Division title with a 45–24 record—tying the franchise record set in 2000 for wins in a half season. Robert Delaney, Brian Dinkelman, Jeff Manship, Wilson Ramos, Anthony Slama, and Danny Valencia represented the Fort Myers Miracle in the 2008 Florida State League All-Star game. Rene Tosoni was also selected for the Western division team, however, a broken leg prevented him from attending. Following the game, Delaney, Dinkelman, Manship & Valencia were promoted to the Twins' Double-A affiliate, the New Britain Rock Cats. Anthony Slama and Wilson Ramos were named to the All FSL team following the season. Manager Jeff Smith was named to the coaching staff.
The second half of the season was won by the Miracle's arch nemeses, the Dunedin Blue Jays. Dunedin had eliminated the Miracle the last three times they made the play offs (& ), and were averaging 5 1/3 runs per game during the regular season. Cole Devries and Alex Burnett both held the Florida State League's most productive offense scoreless over 6.2 and 6 innings, respectively, allowing the Miracle to sweep this best of three series in two games.
Matt Fox struck out ten over six innings in the first game of the FSL championship series to extend the streak of scoreless innings pitched by Miracle starters to 18.2 in the post season. Unfortunately, the bullpen imploded, and he was unable to record the win as the Daytona Cubs defeated the Miracle 5-1. Daytona ended up winning the series in four games.
The Miracle have been affiliated with the following major league teams:
| Year(s) | Affiliate(s) |
|---|---|
| – | Philadelphia Phillies |
| – | Baltimore Orioles |
| Independent | |
| – | San Diego Padres |
| – | Independent |
| –Present | Minnesota Twins |