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Microsatellite loci were isolated and characterized for the endemic fish Chirostoma humboldtianumusing an enrichment procedure. Eight polymorphic microsatellites were genotyped for 32 - 48 individuals from Tepuxtepec Dam, Michoacán. The number of alleles per locus ranged from 3 to 11 and the average observed and expected heterozygosities were 0.61 and 0.63, respectively. All loci deviated significantly from Hardy-Weinberg expectations, which might be related to small population sizes associated to human disturbances and habitat loss. These are the first loci described for the species and the genus and could be useful in studies of population genetics, conservation and management of the species.