Naked common carp (Gymnocypris przewalski) is the only one economic fish endemic to the Qinghai Lake. Recent years, the number of naked common carp has decreased dramatically due to over fishing and deteriorated habitat. In 2004, this fish was listed in China Species Red List as one of endangered species. In this study, we utilized ten polymorphemic microsatellite makers to detect the genetic diversities of six wild populations, abbreviated as BHH, SLH, HEG, QJH, HMH and DSX. Basic data statistics showed that the observed alleles per locus was 2-8 alleles with size ranges of 161-468 bp, the number of effective alleles (Ne) ranged from 1.00 to 5.45, the observed heterozygosity (Ho) from 0.4145 to 0.5105, and the polymorphic information contents (PIC) from 0.383 to 0.4047, respectively. Obviously, the above-mentioned data showed a relatively higher genetic diversity in naked common carp. In addition, the data of genetic similarity and distance showed that there was little differentiation between populations HEG and QJH (DA=00125). The genetic distance was further between populations BHH and DSX (DA= 0.1607). The UPGMA phylogenetic tree showed populations HMH and QJH clustered into one group, and the other four populations converged into the other group.