The aim of the study was to perform comparative analysis of polymorphism of ISSR markers and genetic diversity of rabbit breeds of Poltava silver, Soviet chinchilla and New Zealand white. Methods: The work was performed on the basis of the experimental Cherkasy Biological Resources Research Station of NAAS and the laboratory of the genetics department of the Institute of Breeding and Animal Genetics of NAAS. Genetic passportization of rabbits was performed by amplification of the corresponding genomic DNA sections in the polymerase chain reaction (PCR). Results: Analysis of rabbit DNA multilocus spectra allowed identification of 112 amplified DNA fragments, of which 76 were polymorphic. The basic parameters of genetic diversity of rabbits of three breeds are determined on the basis of their genetic polymorphism. The distribution of intergenerational genetic diversity of GST for ISSR marker (ACC) 6G is 64.3%, (AG) 9C is 48.6%, and (GA) 9C is 52.1%. The average heterozygosity (H) of polylocus DNA markers was: (AG) 9C - 0.165-0.341; (GA) 9C - 0.274-0.342; (ACC) 6G - 0.315-0.318, the proportion of polymorphic loci (P) varied: (AG) 9C - 0.500-0.549; (GA) 9C - 0.674-0.745; (ACC) 6G - 0.710-0.781. Based on the obtained genetic structure, the genetic relationships of rabbit breeds of Poltava silver, Soviet chinchilla and New Zealand white were clustered. Conclusions: An identified unique ISSR marker for rabbits has been identified that can be used to select pairs for hybridization to obtain maximum genetic variation in offspring.