Objective To analyze the population genetics of three groups of closed colony rabbits：Japanese white rabbits(JWR)，Chinchilla rabbits(CR)，and New Zealand rabbits(NZWR)．Methods 18 microsatellite loci were selected and tested by Hardy-Weinberg equilibrium(HWE)，and the values of the allele frequency，observed heterozygosity and expected heterozygosity，the F-statistic value and the genetic distance were counted. Resualts In three populations, the average number of observed alleles respectively are 3.167、4.556、3.444;The average observed heterozygosity respectively are 0.444、0.5230、0.4976;The average polymorphism information content(PIC) respectively are 0.410、0.549、0.470. Four loci showed evident deviation from that of the HWE(P<0.05) and two loci of Sat13 and INRCCDDV0088 are completely homozygous in JWR population; There are two loci evident deviation from HWE in CR and NZW. The genetic distance of CR and NZW is 0.124, while that of CR and JWR being 0.320 and JWR and CR being 0.310. Conclusions Three populations have different genetic characteristics, whose genetic diversity are relatively rich. Several loci are evident deviation from that of the HWE, which probably indicates that certain problems exist in the process of artificial breeding.