The main Creole pig population in Mexico, the hairless Mexican pig, remains as an unimproved and endangered genetic resource. In order to learn more about the genetic characteristics of this pig population, we assessed the allele frequency of 10 microsatellite loci in 177 unrelated hairless pigs from seven regions at Mexico and in 111 pigs of four commercial breeds (Landrace, Large White, Hampshire, and Duroc). Genetic diversity in each population was estimated by the unbiased average heterozygosity and the allele number. Nei's standard genetic distances and a neighbor-joining dendrogram were used to reveal the genetic relationships among these populations. In this report, we present data showing that the level of the genetic diversity in Mexican hairless pigs is high compared with previous reports, and that they belong to a genetic lineage divergent from commercial breeds. Furthermore, Mexican hairless pigs seem to have developed several genetically distinct lines associated with their geographic location. We conclude that the Mexican Creole pig populations may be a reservoir of genetic diversity that is important to preserve and evaluate as a source of new alleles for the future improvement of commercial pig lines.