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In an attempt to characterize the two rabbit breeds concerning the shift on the genetic level we studied microsatellite and genetic markers associated with coat color. These two local rabbit breeds, Nitra rabbit (Ni) and Zobor rabbit (Zo) with different phenotypes have a common origin. Based on the highest polymorphic six microsatellites we chose more than 300 rabbits microsatellites. In two analysed experimental groups Ni (n = 8) and Zo (n = 8) the number of detected alleles for six chosen mikrosatelites was ranged from two to four alleles (4 alleles per INRACCDDV0106, 3 alleles per INRACCDDV0183, 4 alleles per INRACCDDV0259, 4 alleles per Sol08, 2 alleles per SOL28 and 3 alleles per Sol33). Genetic markers were chosen based on the unique characteristics of the two analyzed breeds: mutations c.585delG in the MLPH gene (dilution of coat color), c.5_6insA in the ASIP gene (characters of wild type rabbit) and c.1118C → A in the tyrosinase gene (albinism). The mutation c.585delG in Ni rabbits is represented only by homozygous genotype del/del. Ni is a rabbit breed with a blue-grey coloring, therefore, in principle, other genotype for c.585delG is not expected in this breed. For Zo breed, only G/G homozygous genotype should be represented, but even in that small group of Zo rabbits (n = 8) one heterozygote del/G has occurred, with the recessive allele hidden under the black phenotype. Concerning ASIP gene, from 8 Ni rabbits 7 animals were homozygous ins/ins, which were blue-coated, and only one was Wt/ins, which was Ni wild-blue, whilst Wt/Wt homozygote was not represented. In Ni and Zo breeds the mutation c.1118C → A in the tyrosinase gene was represented only by CC homozygotes, whereas albinos Hyla hybrid was represented only by AA homozygotes. Here we propose steps to make more efficient the process of cross-breeding of the analyzed Ni and Zo rabbit breeds in order to stabilite and then standardize these two unique rabbit breeds, which could could be preserved in the gene bank for possible future use.