Objective To analyze the genetic variation among white hair black eyes (WHBE) rabbit, Japanese white (JW) rabbit and New Zealand white (NZW) rabbit using random amplified polymorphic DNA (RAPD) technique. Methods Thirty rabbits (male/female 1:1) of each strain were used in this study. The genomic DNA was extracted from 90 rabbits. Sixty arbitrary primers were used to amplify DNA of rabbits with RAPD-PCR method. Based on the preliminary experiments, polymorphic primers were selected to analyze the genetic variation among the three rabbit strains. The experimental data were analyzed using Popgene 3.2 software. Results (1) Twenty-five polymorphic primers were selected among 60 arbitrary primers. 493 amplified fragments were detected ranging from 100 bp to 1800 bp. Sixteen primers among 25 arbitrary primers could not only amplify the common DNA bands of 3 rabbit breeds, but also amplify particular alleles in the WHBE rabbit. (2) 234 RAPD sites were detected by agarose gel electrophoresis in WHBE rabbit, among which 166 sites were polymorphic, accounting for 70.94%. 228 RAPD sites were detected by agarose gel electrophoresis in the JW rabbit, while 122 sites of them were polymorphic, accounting for 53.51%. 231 RAPD sites were detected by agarose gel electrophoresis in the NZW rabbits, with 94 sites being polymorphic, accounting for 40.69%. (3) The Shannon genetic diversity index of WHBE rabbit, JW rabbit and NZW rabbit was 0.3385, 0.2222 and 0.1905, respectively. (4) The genetic similarity between JW rabbit and NZW rabbit was highest among the three rabbit breeds (0.8443), followed by that between WHBE rabbit and JW rabbit (0.8204), and the genetic similarity between WHBE rabbit and NZW rabbit (0.7862) was the lowest. Conclusions Our results demonstrate that there are both genetic similarities and genetic variations among WHBE rabbit, JW rabbit and NZW rabbit. The RAPD technique can be used to delect the genetic relationships among different breeds and different individuals of the same breed of rabbits.