This study was aimed to analyze the genetic diversity of Alashan Gobi Bactrian camel using microsatellite markers,find the microsatellite markers which associated with body size trait,and provide reference for marker-assisted selection of Alashan Gobi Bactrian camel.17 microsatellite markers were selected to detect the polymorphism in Alashan Gobi Bactrian camel population by non-denaturing polyacrylamide gel electrophoresis technique,and the correlation analysis was performed between microsatellite markers and body size traits.The results showed that 60 alleles were detected in 17 microsatellite markers,the average effective allele number was 2.7302,the average heterozygosity was 0.6205,the average polymorphic information content was 0.5308,which indicated that the genetic diversity of the Alashan Gobi Bactrian camel population was rich.The correlation analysis results indicated that 8 microsatellite markers (LCA82,LCA90,CMS15,CMS36,CMS104,CVRL01,YWLL36 and YWLL44) were associated with different body size traits,especially CMS36 and YWLL44,which were related to all body size traits.For CMS36 marker,there was significant difference between different genotypes and body length (P<0.05),the order was BB > AA > AB,the body height,chest circumference and cannon circumference of AA and BB genotypes were significantly higher than that of AB genotype (P<0.05).For YWLL44 marker,the body height,chest circumference and body weight of AC genotype were significantly higher than that of BD genotype (P<0.05),the body length of AC genotype was significantly higher than that of AB and BD genotypes (P<0.05),and the chest circumference of AB and AC genotypes was significantly higher than that of BD genotype (P<0.05).Summarily,8 microsatellite markers including LCA82,LCA90,CMS15,CMS36,CMS104,CVRL01,YWLL36 and YWLL44 had certain effects on the body length of Alashan Gobi Bactrian camel,CMS36 and YWLL44 had influence on the body height;LCA82,LCA90,CMS36,CVRL01,YWLL36 and YWLL44 had influence on the chest circumference;LCA82,CMS15,CMS36,CMS104,CRVL01 and YWLL44 had influence on the cannon circumference;LCA82,LCA90,CMS15,CMS36,CVRL01 and YWLL44 had influence on the body weight.