Kostyakova, Moscow, 127422 Russia, e-mail vglazko@yahoo.com Received March 31, 2014 Abstract Using sequences of mobile genetic elements in order to mark polymorphic sites in their insertion might be the most effective approach to identify specific features of gene pools of different groups of organisms and control their dynamics, which is especially important in dealing with agricultural species. <...> Sireviruses (Pseudoviridae) one of the oldest LTR-retrotransposons are widespread throughout the plant kingdom. <...> SIRE-1 is one of the largest and most detailed studied retrotransposon. <...> Its analysis showed that insertions of the retroelement (particularly in the genome of maize) have occurred recently. <...> We studied the polymorphism of DNA fragments flanked by LTRretrotransposon SIRE-1 (IRAP-PCR markers) in the genomes of different taxonomic groups. <...> The objects of our study were Triticum aestivum (Moscovskaya 39, Mironovskaya 808, Omskaya 36 varieties), Glycine soja (five wild populations of Primorskii region of Russia) and G. max (China), as well as representatives of the factory and indigenous breeds of cattle — Black-and-White cattle improved by Holstein cattle, Ayrshire, Yakut and Red Estonian cattle (97 animals in total). <...> A terminal site of SIRE-1 was chosen as primer in IRAP-PCR (GCA-GTT-ATG-CAA-GTG-GGA-TCA-GCA). <...> The data indicate that the multiloci genotyping by IRAP-PCR using retrotransposon LTR SIRE-1 as a marker reliably differentiates not only representatives of the monocotyledonous and dicotyledonous plants, but also their varieties. <...> Spectrum of DNA fragments (13 to 16 depending on the breed) obtained in studies different breeds of cattle using IRAP-PCR markers was in the length range of 330-1470 bp. <...> The highest polymorphism of DNA fragments was observed in the middle part of the spectrum (760-980 bp) in Ayrshire and Black-and-White cows. <...> According to the obtained dendrogram one of the groups of Black-and-White cows and Ayrshire cattle were closer to each other, while the other with Red Estonian and Yakut cattle became isolated in a separate subcluster. <...> Identified differences in heterogeneity in the two studied groups of Black-and-White from different farms possibly could be explained by the peculiarities of breeding work carried out or with other factors of artificial and/or natural selection. <...> The possibility of using LTR-retrotransposons as molecular genetic markers for polyloci genotyping plants and animals is discussed. <...> Keywords: inverted <...>