Wayne Huizenga, CEO of Blockbuster Entertainment Corporation, was awarded an expansion franchise in the National League (NL) for a $95 million expansion fee and the team began operations in 1993 as the Florida Marlins. MLB had announced a few months earlier that it intended to add two new teams to the National League. It was a foregone conclusion that one of them would be placed in Florida; the only question was whether Huizenga would beat out competing groups from Orlando and Tampa Bay. Orlando fielded a very spirited campaign bolstered by its family-oriented tourism industry. Tampa Bay already had a baseball park—the Florida Suncoast Dome in St. Petersburg, completed in 1990. However, on June 10, 1991, the National League awarded a Miami-based franchise to Huizenga. The franchise adopted the nickname "Marlins" from previous minor league teams, the Miami Marlins of the International League from 1956 to 1960, and the Miami Marlins (1962–70) and Miami Marlins (1982–88) teams that played in the Florida State League.
In 1997, the Marlins finished nine games back of the Division Champion Atlanta Braves, but earned the wild card berth. Veteran additions such as LF Moisés Alou, 3B Bobby Bonilla, and trade-deadline additions Darren Daulton and Jim Eisenreich added experience and clutch hits. Talented young stars Luis Castillo (2B) and Édgar Rentería (SS) comprised one of the best double play combos in the NL. The Marlins swept the San Francisco Giants 3–0 in the National League Division Series, and then went on to beat the Atlanta Braves 4–2 in the National League Championship Series, overcoming the loss of Alex Fernandez to a torn rotator cuff, and Kevin Brown to a virus. Brown's place was taken in Game 5 by rookie pitcher Liván Hernández, who struck out 15 Braves and outdueled multiple Cy Young Award winner Greg Maddux to a 2–1 victory. The underdog Marlins went on to face the Cleveland Indians in the 1997 World Series, and won in seven games. In Game 7, Craig Counsell's sacrifice fly in the bottom of the ninth tied the game at 2, then, with the bases loaded and two outs in the bottom of the 11th, Édgar Rentería's soft liner glanced off the glove of Cleveland pitcher Charles Nagy and into center field to score Counsell and give the Marlins the win.
On May 9, the Marlins called up high-kicking southpaw Dontrelle Willis from the Double-A Carolina Mudcats and helped carry the injury-plagued Marlins with an 11–2 record in his first 17 starts. Miguel Cabrera (also from the Mudcats) filled in well, hitting a walk-off home run in his first major league game, against the Tampa Bay Devil Rays at Pro Player Stadium. Both Willis and Cabrera would later prove to be essential parts of the Marlin's playoff success. Jeff Conine – an original Marlin and member of the 1997 World Series team – returned from Baltimore, and closer Ugueth Urbina arrived from the Texas Rangers. These acquisitions helped to keep the team in contention, and although they finished ten games behind the Braves, the Marlins captured the NL wild card.
On October 15, the Marlins defeated the Chicago Cubs four games to three in the Championship Series, coming back from a 3–1 deficit. Game 6 saw the Marlins play a role in one of baseball's most infamous moments: "The Inning". With 1 out in the 8th inning and the Cubs 3 runs ahead, Marlins 2nd baseman Luis Castillo hit a pop foul a row into the stands along the third baseline. Cubs fan Steve Bartman reached for the ball, preventing Cubs LF Moisés Alou from making the out and setting off an 8-run Marlins rally. The incident with Steve Bartman and a come-from-behind win in Wrigley Field in Game 7 helped the Marlins capture their second NL pennant, keeping the "Curse of the Billy Goat" alive and well.
In the 2003 World Series, the Marlins defeated the heavily favored New York Yankees in six games, winning the sixth game in Yankee Stadium. Shortstop Álex González helped the Marlins in Game 4 of the series with a walk-off home run in extra innings. Josh Beckett was named the Most Valuable Player for the series after twirling a five-hit complete-game shutout in Game 6. Skipper Jack McKeon became the oldest manager ever to win a World Series title.
In 2012, the team moved from the football-oriented Sun Life Stadium (located in Miami Gardens) to Marlins Park in downtown Miami. As a condition of the move, the team was renamed the Miami Marlins, and adopted a new logo and colors.
The Marlins won the World Series in 1997 and 2003, but both titles were followed by controversial periods where the team sold off all the high-priced players and rebuilt. Between 2003 and 2019, the team's two World Series runs also marked their sole postseason appearances. Their three playoff qualifications and seven winning seasons are the fewest among MLB franchises.
On November 13, 2020, the Marlins became the first club in any American major-level sports league to hire a woman to an executive position when Kim Ng was announced as the team's general manager. In addition, she will also be MLB's first Asian American general manager