On June 10, 1991, the National League awarded a franchise to Wayne Huizenga, chief executive officer of Blockbuster Entertainment Corporation, owner of the Miami Dolphins football team, and chairman of the board of the Florida Panthers hockey team. The Marlins' first manager was Rene Lachemann, a former catcher who had previously managed the Seattle Mariners and Milwaukee Brewers. Lachemann kept Florida out of the Eastern Division cellar during the 1993 season as the team finished the year five games ahead of the last-place New York Mets. After the Marlins finished last in their division in 1994 and fourth in 1995, Lachemann was replaced as manager midway through the 1996 season with the Marlins' director of player development, John Boles.
Despite problems in the dugout and on the field, the Marlins had some bright spots on the mound and behind the plate in 1996. The team's 3.95 ERA ranked third in the NL, led by newcomer Kevin Brown, who finished the season with a 17-11 win-loss record and an impressive 1.89 ERA. Catcher Charles Johnson led the league with a .995 fielding percentage, threw out a league-high 48 percent of base runners, and collected his second straight Gold Glove Award for fielding excellence. After a slow start, the Marlins finished the year with an 80-82 win-loss record to place third in their division. Boles then returned to his previous position as director of player development, and former Pittsburgh Pirates manager Jim Leyland was hired to lead the club in 1997.
The Marlins got their second no-hitter from ace Kevin Brown. The first coming in 1996 by Al Leiter. With those two starters and an almost automatic closer in Robb Nen, the Marlin's staff was almost systematic during their regular season run. In 1997, the Florida Marlins led by new manager Leyland won the wild card, finishing 92-70. RF Gary Sheffield followed his 40 HR 120 RBI season with a .250 average but 6 million dollars richer. Veteran additions such as CF Devon White, 3B Bobby Bonilla, and Darren "Dutch" Daulton added experience and clutch hits. Talented young stars and starters Louis Castillo (2B) and Edgar Renteria (SS) were one of the best double play combos in the League. Castillo was injured and replaced by Craig Counsell before the playoffs began. They 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.
The underdog Florida Marlins went to take on the Cleveland Indians and won the 1997 World Series in 7 games, with an amazing extra-inning single by shortstop Edgar Rentería off of Cleveland pitcher Charles Nagy, which barely cleared his glove, scoring Craig Counsell to win the game. Liván Hernández was named the MVP.
Following the World Series victory team owner Wayne Huizenga claimed massive financial losses which would later prove to be mostly false as he reported team and stadium earnings separately. He dismantled the team by trading off most of the club's most talented players. Among them, Moises Alou was traded to the Houston Astros, Bobby Bonilla was traded to the Los Angeles Dodgers, and Kevin Brown was traded to the San Diego Padres. Fans were outraged by this "fire sale", some comparing it to Blockbuster Video selling used tapes at bargain rates. Some disgruntled fans came up with the slogan, "Wait 'til last year!" Marlins home attendance plummeted.
The Marlins' record in 1998 slumped to 54-108, making them the first club ever to win a World Series and then lose more than 100 games during the following season. Leyland resigned as manager in October 1998, and Huizenga sold the club to businessman John Henry during the off-season. In 2002, the Marlins' fifth straight losing season since winning the World Series, the team drew a franchise low 813,111 fans, averaging just 10,038 per game.
The club slowly worked back to becoming a respectable ballclub despite attendance issues, driven by young stars such as A.J. Burnett, Luis Castillo, and Mike Lowell. From 2000 through 2002, the Marlins consecutively put up three 75+ win seasons. In 2002, Tony Pérez was replaced by Jeff Torborg as the new Marlins manager. Torborg put up a 79-83 record in his first season with the team.
In the offseason, the Marlins acquired 10-time Golden Glove winner Iván Rodríguez from free agency and Juan Pierre from the Colorado Rockies after trading off homerun sluggers Cliff Floyd and Preston Wilson.
The Marlins struggled in the opening stages of the season, going 16-22. In that span, Florida also lost its top three pitchers, A.J. Burnett, Josh Beckett, and Mark Redman. On May 11, Florida replaced manager Torborg with 72-year-old Jack McKeon. In that timespan, Florida was at its lowest point, with a major league worst record of 19-29.
Around the same time, Florida recalled the high-kicking rookie phenom Dontrelle Willis up from the Double-A Carolina Mudcats, who carried the injury-plagued Marlins with a 9-1 record in his first 13 starts. Miguel Cabrera (also from the Mudcats), Jeff Conine (from Baltimore) and Ugueth Urbina (from Texas) were all acquired mid-season as well to help the Marlins play-off push. Finally, Florida clinched the National League Wild Card for the second time in team history with a 4-3 win over the New York Mets on September 26, finishing with an overall record of 91-71.
The Marlins clinched the Division Series against the favored San Francisco Giants going 3 games to 1. In the two Division Series games at Pro Player Stadium, Florida drew over 130,000 fans. The series ended with Marlins catcher Rodríguez tagging out a charging J.T. Snow at the plate after catching a perfect throw from Jeff Conine, which made it just in time to make the play. Snow, the son of former Rams lineman Jack Snow, tried to imitate his father by lowering his shoulder and bulldozing Rodríguez at the plate, but the Marlins catcher held on to the ball for the out. It was the first postseason series ever to end with the potential tying run being thrown out at the plate. On October 15, the Marlins defeated the Chicago Cubs four games to three in the 2003 National League Championship Series, after falling three games to one before coming back with a Beckett complete-game shutout in Game 5; The Inning, in Game 6, and the traditional come-from-behind win in Game 7 to take the series, staking claim to their second NL pennant and advancing to the 2003 World Series, where they defeated the New York Yankees in six games. Starter Josh Beckett was named the Most Valuable Player for the series after twirling a five-hit complete-game shutout in Game 6.
- Dontrelle Willis named NL Rookie of the Year
- Jack McKeon named Manager of the Year
- Derrek Lee traded to Chicago Cubs for Hee Seop Choi
- Iván Rodríguez up for free agency (signed by the Detroit Tigers)
Although posting a winning record of 83-79 (only their third winning season of their history), the Marlins' aspirations of successfully defending their World Series title fell short as they finished nine games behind the Houston Astros for the National League Wild Card title, thus the Marlins became the fourth consecutive major league team not to repeat as World Series champions.
A series of rain-outs in September (due to hurricanes in Florida), the delayed doubleheaders that followed, and losing three key players from the Marlins' previous championship year (Rodríguez, Lee and Urbina) factored in the team's downfall during the season's stretch run.
But the team was able to retain Jack McKeon as manager for the 2005 season.
While losing All-Stars Carl Pavano and Armando Benitez in the off-season, the Marlins signed P Al Leiter and 1B Carlos Delgado. Delgado's contract was the biggest in franchise history at $52 million over 4 years, with an option for a fifth year. Meanwhile, play-by-play TV broadcaster Len Kasper was also lost to the Chicago Cubs and replaced by Rich Waltz (who had previously been with the Seattle Mariners), and radio announcer Boog Sciambi was replaced by Roxy Bernstein.
With the addition of Delgado, the Marlins were expected to finish at either first or second in the NL East by many sportswriters. However, at the All-Star break this season, they were 44-42; and the NL East was unusually competitive, as all five of its teams had a winning record at the break. The Marlins, then, have been criticized for underachieving in the first half of the 2005 season. While Cabrera, Willis, and several others posted very good first-half numbers, Lowell was one of the worst offensive producers among regular major-league starters, and Leiter went 3-7 with an ERA of 6.64 before being traded to the New York Yankees on July 15 for a player to be named later. Additionally, Guillermo Mota, who was acquired in 2004 along with Paul Lo Duca and Juan Encarnacion and was expected to be their closer, has been inconsistent, and the Marlins gave the closer job to veteran Todd Jones, whom they signed in the offseason. However, the Marlins did send four players to the All-Star Game (Willis, Lo Duca, Castillo, and Cabrera), tying a team record.
The club was expected to be quite active at the trading deadline (July 31), as Burnett is a free agent after the season and had already said that he wants to test the market like Pavano did rather than stay in Florida. Burnett was mentioned in possible trades with the Chicago White Sox, Boston Red Sox, New York Yankees, Toronto Blue Jays, and Texas Rangers, with many rumors also including Lowell or Encarnacion. There were also rumors that Jack McKeon might be fired, with former Marlins manager Jim Leyland and Yankees bench coach Joe Girardi being among the rumored replacements. The Marlins did not make a huge move at the deadline, instead trading minor-leaguers Yorman Bazardo and Mike Flannery to the Seattle Mariners for left-handed pitcher Ron Villone.
The Marlins did have some pleasant surprises during the season. Dontrelle Willis became the 13th member of the Black Aces when he defeated the Washington Nationals to earn his 20th win. He finished the season 22-10 with a 2.63 ERA, and he was considered a favorite to win the Cy Young Award for much of the season. Also, Jones, a journeyman who had been signed as a setup man, had one of the best years of his career as a closer; he earned 40 saves and had a 2.13 ERA. In addition, late-season callup Jeremy Hermida, a highly-regarded prospect who has been compared to Jeff Francoeur, hit a grand slam in his first major-league at-bat and a game-tying two-run homer in the last game of the season.
The Marlins led the NL wild-card race as late as September 13, but they then lost 12 of their next 14 games. Added to the controversy was the September 26 dismissal of A.J. Burnett from the team for making disparaging comments about the Marlins' lack of offense, their "scared" ways of playing and coaching, and Jack McKeon's management of the team. The Marlins closed the season by sweeping the Atlanta Braves, and their final record for the season stood at 83-79.
McKeon, still the oldest manager in the majors at age 74, announced his retirement on October 2 after the Marlins' last game of the season. Former Tampa Bay Devil Rays manager Lou Piniella, Braves third base coach Fredi Gonzalez (who previously managed in the Marlins' farm system), and New York Yankees bench coach Joe Girardi have been named as possible replacements for McKeon.  On October 19, they hired Girardi as their new manager. Girardi, who they hired at age 41, became the youngest current manager in the major leagues. 
Few of the coaching staff, aside from infield/first base coach Perry Hill and bullpen coordinator Pierre Arsenault, are expected to return; Marlins GM Larry Beinfest has told them to seek employment elsewhere. Pitching coach Mark Wiley and bullpen coach Luis Dorante came under fire during the season due to the late-season struggles of Burnett and the season-long struggles of the Marlins' bullpen. Similarly, hitting coach Bill Robinson was often blamed for the Marlins' offensive woes throughout the season, and in particular his failure to get Pierre and Lowell out of season-long slumps. Girardi is considering Andrés Galarraga as a replacement for Robinson.
On October 3, the first day after the end of the regular season, the Marlins made their first offseason moves, releasing relief pitchers John Riedling and Tim Spooneybarger. Riedling had a 4-1 record and a 7.14 ERA during the season; Spooneybarger, who had not played since 2003 due to rehabilitation from Tommy John surgery, had to have the surgery a second time during the season and is expected to miss at least the 2006 season as well. Reliever Jim Mecir retired following the Marlins' last game of the season.
Todd Jones, A.J. Burnett, Jeff Conine, Lenny Harris, Juan Encarnacion, Alex Gonzalez, Brian Moehler, and Ismael Valdez are among the Marlins players whose contracts expired following the 2005 season. Following the playoffs, they will be able to declare free agency.
- Founded: 1993 (National League expansion)
- Uniform colors: Black, Gray, Teal, and White; some Orange
- Logo design: Circle design with "FLORIDA" and "MARLINS" written around it; a marlin jumping through the circle and a baseball in the background.
- Cable Television Network: Fox Sports Net Florida (FSN Florida) is the Florida Marlins home television channel. PAX also shows Marlin games sometimes. The FSN Florida slogan is "Get Hooked" (only for the Marlins).
- Playoff appearances (2): 1997, 2003
- Official Television Stations: FSN(Florida),PAX
- Official Radio Stations: WQAM (560)
Though the Marlins have never won a division title, they have also never lost a playoff series in their history (a perfect 6-0).
- Tony Pérez (manager)
Minor league affiliations
- AAA: Albuquerque Isotopes, Pacific Coast League
- AA: Carolina Mudcats, Southern League
- Advanced A: Jupiter Hammerheads, Florida State League
- A: Greensboro Grasshoppers, South Atlantic League
- Short A: Jamestown Jammers, New York-Penn League
- Rookie: GCL Marlins, Gulf Coast League
- Rookie: VSL Marlins Universidad, Venezuelan Summer League
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- CapeFish's Marlins Ballpark News