Abstract: The genetic diversity of eight microsatellite sites was studied by PCR, and the allele frequency, polymorphism information content (PIC), heterozygosity (H) and effective number of alleles (Ne) in different rabbit populations were analyzed with statistics method. At the same time, the cluster of these rabbits has also been studied. The results were showed as follow that (1) The eight microsatellite sites were high polymorphism in six rabbit populations. The average PIC in each site was 0.6622 (0.5723-0.7222). The difference of average PIC among these populations was not significant. The average heterozygosity in all populations was 0.6857 (0.5904-0.7267). These results indicated that there was a good compatibility between PIC and H in different six rabbit populations. It also showed that there was rich in genetic polymorphism of microsatellite sites within Fujian yellow rabbit. (2) According to the Neis standard genetic distance, the UPGMA dendrogram indicated that there were little genetic difference among six populations. There was rich in genetic polymorphism of microsatellite sites within Fujian yellow rabbit. This cluster result showed that these populations clustered into the same breed.