Cherax quadricarinatus is a decapod crustacean of interest to the aquaculture industry. In Mexico, a significant effort has been made to improve biological requirements, but the genetic characteristics are unknown. We examined the genetic diversity and differentiation in four populations in Mexico (three commercial farms and one feral population), as well as one research line from Argentina, used as reference. To initiate a founder stock in a genetic improvement program, we analyzed five microsatellite markers. The genetic diversity in terms of the number of alleles was low to moderate (2.8-6.2) in Mexican populations than the Argentinean sample (8.8). A pairwise Wright's Fst analysis showed that all populations were significantly different (P < 0.5). Cross-breeding organisms from a different population are suggested to increase genetic variability before initiating a founder stock with higher genetic variation.