The paper discusses the possibilities of effective application of the terminal fragments of transposable elements of flowering plants and mammals as primers in IRAP-PCR to study the genetic structure of local breeds of sheep and horses in order to determine the gene pool "standard" of breed. Breed-specific loci differed in polymorphic information content (PIC) were found for each of the study groups of sheep and horses. Fragments specific in PIC of each of the studied groups from three different farms of Altaic horses were detected. Besides loci differentiated two inbreeding types of Edilbai sheep in different ecological and geographical conditions were found. Phylogenetic differentiation of breeds and inbreeding groups did not always coincide with the known history of the origin and depended on the primer. Variety-specific fragments have been identified as a result of genotyping wheat varieties using a site of LTR SIRE-1 as a primer. The dendrogram constructed on the basis of values of genetic distances reflects both the phenotypic characteristics of each of the varieties and their origin. The spectra of the fragments obtained by PCR with primer LTR SIRE-1 also distinguish two species of soybean (G. max and G. soja), as well as representatives of G. max.
