The team was founded on October 8, 1970, and its home stadium was Estadio Tomás Oroz Gaytán (1971-2015) in October 2016 the new stadium opens. They have been champions of the league on six occasions. The first time was at the 1965–1966 season with Manuel Magallón (Mexico) as coach. The next two occasions were on the 1972–1973 season (coach Dave Garcia, United States) and the 1980–1981 season (coach Lee Sigman, United States). On January 27, 2008 Yaquis won their fourth championship, defeating Venados de Mazatlán 4 games to 1, with Homar Rojas (México) as manager.

Managed by Eddie Díaz (Dominican Republic), the Yaquis won the 2010-11 championship, defeating Algodoneros de Guasave 4 games to 3, and went on to win the 2011 Caribbean Series contested in Mayagüez, Puerto Rico. The Yaquis won a second consecutive season after winning the 2011-2012 championship under Eddie Díaz (Dominican Republic). The Yaquis are the first team of the Liga Mexicana del Pacífico to win three straight championships. They won the 2012-2013 championship under Eddie Díaz (Dominican Republic) and went on to win the 2013 Caribbean Series, their second in three years. The 2013 Caribbean Series was the first to feature a final game after a Round-robin tournament. The final game lasted 18 inning ending at 2 am local time.

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