Bashania fargesii as one of the main staple food bamboos for giant panda in Tsinling Mountains has been protected by the Chinese government. 15 microsatellite primers were developed in B. fargesii and B. aristata for studying phylogenetic relationships, population clonal structure and genetic diversity. All of these loci showed polymorphisms, and the number of alleles per locus ranged from 4 to 20 from two populations. The observed and expected heterozygosities ranged from 0.310 to 0.981 and from 0.323 to 0.905, respectively. The polymorphic information content ranged from 0.322 to 0.901. These primers will useful to study the phylogenetic relationships, population clonal structure and genetic diversity of B. fargesii and B. aristata.