In this study, 17 microsatellite markers were used to analyze the genetic polymorphism, genetic differentiation, gene flow and genetic distance of Alashan desert Bactrian camel, Alashan Gobi Bactrian camel, Sunite Bactrian camel and Qinghai Bactrian camel.The results indicated that the number of effective alleles of the four Bactrian camel varieties ranged from 2.7302 to 3.0524, and average theoretical heterozygosity and average polymorphic information content were 0.6283 and 0.5546, respectively. Observational heterozygosity, expected heterozygosity and polymorphic information content of Qinghai Bactrian camel were all higher than those of the other three varieties, being 0.8922, 0.6490 and 0.5813, respectively, so Qinghai Bactrian camel was of rich genetic polymorphism. Average gene flow of the microsatellite markers was 12.3188 and average Fst value was 0.0199, namely 1.99% of genetic variation derived between subpopulations and 98.01% came inside the subpopulations, revealing that the genetic differentiation degree between Bactrian camel subpopulations was low. The genetic relationship between Sunite Bactrian camel and Alashan Gobi Bactrian camel was close, so it was classified into the first type and that between Sunite Bactrian camel and Alashan desert Bactrian camel as the second type, but the genetic relationship of Qinghai Bactrian camel and other three Bactrian camel varieties was distant.