Genetic diversity among two genetic groups (New Zealand White and APAU Black) was investigated with a set of 20 microsatellite markers in the present study. The results showed that out of 20 microsatellites, 12 rabbit specifi c markers were successfully amplifi ed by PCR which were highly polymorphic. A total of 257 alleles were observed across the 12 loci amplifi ed. Number of alleles ranged from 5 to 14 and 5 to 16 in New Zealand White and APAU Black populations, respectively. The overall mean values of observed heterozygosity (0.554 in New Zealand White and 0.556 in APAU Black), expected heterozygosity (0.870 in New Zealand White and 0.875 in APAU Black), Polymorphic Information Content (0.856 in New Zealand White and 0.862 in APAU Black) and the mean effective number of alleles (8.629 in New Zealand White and 8.876 in APAU Black) of these two genetic groups were high. Out of the 12 amplifi ed loci 7 loci deviated signifi cantly from Hardy - Weinberg equilibrium in New Zealand White and 5 loci deviated in case of APAU Black which may be due to selection followed. The mean FIS, FIT and FST values over all the population were found to be 0.377, 0.402 and 0.040, respectively. The results suggested that the 12 amplified rabbit specific microsatellite loci were effective markers for analysis of genetic relationships among rabbit populations.