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Unicaja was originally founded in 1977, as CB Caja de Ronda. In 1992, the club merged another ACB team in the city of Málaga, CB Maristas de Málaga, which was originally founded in 1953 as Ademar Basket Club. Over the years, the club has featured players like: Nacho Rodríguez, Berni Rodríguez, Carlos Cabezas, Jorge Garbajosa, Marcus Brown, Sergei Babkov, Michael Ansley, Louis Bullock, and Kenny Miller, as well as numerous other well-known players. The club won its first title, when it won the European-wide third tier level FIBA Korać Cup in the 2000–01 season. They then won the Spanish King's Cup title in 2005. The next year, in the 2005–06 season, Unicaja won its first-ever Spanish League championship.

The club finished its best years to date, by qualifying for the 2007 Euroleague Final Four, where it was defeated in the semifinals by CSKA Moscow, and thus finished in third place in the EuroLeague. In October 2007, Unicaja faced the NBA's Memphis Grizzlies in a friendly match, and they defeated the Grizzlies, by a score of 102–99. That was one of the 17 times that an NBA team has lost to a foreign club. Pau Gasol and Juan Carlos Navarro, two of the greatest Spanish basketball players of all time, played for Memphis in that historical game.

Málaga participated in the European-wide top-tier level league, the EuroLeague, for 15 consecutive seasons (2001–02 season to 2015–16 season). However, in the summer of 2015, it lost its EuroLeague A-licence. Therefore, in the 2016–17 season, Unicaja participated in the second tier level EuroCup. The club immediately won the EuroCup title, in its first season in the league, after winning over Valencia Basket in the league's Finals.