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.