Analysing genetic diversity of Apis cerana cerana and Apis mellifera ligustica in China could provide a theoretical foundation for the research on the conservation and reasonable utilization of honey bee populations, but there have not public reports on this topic by using microsatellite markers until now. Genetic diversity of Changbaishan bee (Apis cerana cerana) and Pinghu royal jelly bee (Apis mellifera ligustica) in China were evaluated with 21 microstaellite loci, the genetic variability within breeds and genetic differentiation between breeds were estimated, the results showed that in 21 microstaellite loci, 171 alleles were found, the number of alleles per locus ranged from 3-13, the average expected heterozygosity and PIC of all loci were 0.7175 and 0.6755, respectively. Mean numbers of alleles of Changbaishan bee and Pinghu royal jelly bee were 1.86 and 6.27, the average of genetic differentiation measured as FST value, was 51.9% (p<0.001) and all loci contributed significantly (p<0.001) to this differentiation. It can also, be seen that the deficit of heterozygotes was very high (0.574) (p<0.001). Reynolds distance values between 2 populations were 0.734.