A polymorphism of microsatellites in semi-fine wool sheep in the Romney Marsh type of the Pechora population (bred with the involvement of now extinct northern short-tailed indigenous sheep) is studied. Estimation of the differentiation of sheep groups of different genesis by the frequencies of STR loci genes, identification of private alleles, and cluster analysis do not allow information about the allele fund of the indigenous sheep to be obtained. Apparently, absorption crossing into an improving breed with the selection of a crossbred population according to the target standards of meat–wool breeds leads to loss of the gene pool typical for the northern indigenous sheep by the Pechora semi-fine wool sheep.