Objective To analyze the population genetics of three closed rabbit colonies:Japanese white rabbits (JWR), Chinchilla rabbits (CR), and New Zealand rabbits (NZWR). MethodsTen 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. ResultsThe microsatellite locus 12L1E11 in CR population, the loci INRACCDDV0087 and INRACCDDV0203 in NZWR population, and the loci Sat12 and INRACCDDV0203 in JWR population showed evident deviation from that of the HWE (P<0.05), mostly resulted from heterozygote deficiency. All the other microsatellite loci Sat13, Sol4,6L1F0,7L1F1,2L4A1, and INRACCDDV0016 in the three populations consisted with that of the HWE. The average number of alleles was 5.9, and the range of allele frequencies was from 0 to 0.9060. The average observed heterozygosity was 0.6204 and the average expected heterozygosity was 0.6178. The average Fst value among populations was 0.0750. The observed lowest genetic distance was 0.1223 between JWR and CR,and the observed highest genetic distance was 0.1934 between CR and NZWR. ConclusionsThe genetic structures of the three closed rabbit colonies show genetic stability and homogeneity. The 10 microsatellite loci have high genetic polymorphisms. There is evident genetic differentiation among populations.