The Miami Marlins have a relatively short history, joining Major League Baseball as an expansion team in 1993. They made good use of their first decade, though, winning World Series championships in both 1997 and 2003.
Outside of those two seasons, however, they have a pretty lackluster history, which made this post pretty easy. In fact, those two years are the only times the Marlins have ever made the playoffs.
Both seasons are actually fairly even when you compare them. In 2003 the Marlins finished the year 91-71 and with a run differential of 59. In 1997, they finished 92-70 and with a run differential of 71.
Both years saw the Marlins finish in second place in their division, but go on to a postseason run and win the World Series.
Due to that one extra win and a marginally better run differential, I'm going with the 1997 Marlins as the best season in franchise history. The team that won the first World Series for the franchise also produced three All-Stars: Moises Alou, Kevin Brown and Charles Johnson.
Darren Daulton, who batted .262/.371/.429 that season, was named National League Comeback Player of the Year.
The '97 Marlins are one of those teams that show you how important momentum is and how random the postseason can be. Despite posting a great record and the third most wins in the league, the only major offensive category in which they finished in the top 10 was on base percentage (.346).
Their pitching is what carried the team, as they finished fourth in ERA and fifth in strikeouts among teams in the league in 1997. Brown led the team with a 16-8 record, 2.69 ERA and 205 strikeouts on the year.
The Marlins started off well with two championship seasons within their first 11 years, but they have yet to make the postseason since. At least they'll always have the 1997 and 2003 seasons to hang on to.