Flores, who had been in charge for 18 months, became the club's eighth coaching casualty since flamboyant businessman Jorge Vergara bought Guadalajara in 2002.
Mexico's most popular club and the only one not to field foreign players said in a statement that the rest of the technical staff would keep their jobs.
The Chivas, who lost 1-0 to UANL Tigres at the weekend, are fifth out of six teams in Group Two of the Mexican Clausura championship although they lead their group in the South American Libertadores Cup with six points from three matches.
Vergara, seen as an upstart by the Mexican business establishment who deplore his habit of not wearing socks, said he would turn Guadalajara into the world's biggest club when he bought it in 2002.
Since then he has co-founded MLS club Chivas-USA to draw on the large Mexican community in Los Angeles and is owner of Costa Rican club Saprissa.
Guadalajara have won one Mexican title since Vergara took charge. Two separate championships are played every season.
Daniel Guzman, Hans Westerhof (twice), Xavier Azkargorta, Jose Manuel de la Torre, Benjamin Galindo and Eduardo de la Torre are the other coaches to have lost their jobs under Vergara.
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