Abstract: This study analyzed genetic variation of major histocompatibility complex（MHC）Ⅱ gene exon 2 in 30 Ziwuling black goats, in order to obtain the information of MHCⅡ gene polymorphisms and the relationship between MHCⅡ gene and the body size traits of Ziwuling black goat, so as to evaluate the population development trend and lay a foundation for the research on the correlation between MHCⅡ gene and growth performance or disease resistance, and promote the protection, development and utilization of Ziwuling black goat. A total of 4 kinds of MHCⅡ gene exon 2 sequences were obtained, including DQA2, DRB1, DQB2 and DRA. Polymorphism analysis found that gene polymorphisms were abundant except DRA. During the long-term evolution, DRB1 and DQB2 genes were subjected to obvious selection pressure, which contributed to the adaptation of Ziwuling black goats to local climate. The body size indexes of Ziwuling black goats were lower than those of Shanbei white cashmere goats. It was found that the distribution of DQA2 genotype of two populations was different at 0.05 level and the distribution of DRB1 allele and genotype of two populations was different at 0.01 level. The study on MHC gene polymorphism of Ziwuling black goats can help to screen MHC candidate genes related to growth or disease resistance, and thus promote the protection and strain improvement of Ziwuling black goats.