The comparative analysis of genetic structures of five cattle breeds has been carried out using polymorphism of two different types of molecular-genetic markers – 20 structural genes and 128 DNA loci (the DNA fragments flanked by inverted microsatellite loci repetitions – ISSR-PCR method). In spite of availability of breed-specific singularities of genotype distribution detected by the both methods the level of mean heterozygosity of structural genes was similar in all the investigated breeds. A part of polymorphic loci and the average value of the polymorphic information contents (PIC) of ISSR-PCR markers has appeared much higher in commercial breeds with high effective number in comparison with Ukrainian autochthonous breeds. The population-genetic processes detected by different methods are discussed.
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