Sheep were one of the first animals to be domesticated. The history of sheep domestication and their widespread distribution dates to about ten thousand years ago, during which sheep exhibit both physical changes and modifications at the genetic level. The authors developed a system of 49 oligonucleotide primers for targeted Next Generation Sequencing (NGS) of genetic loci for phylogenetic analysis and identifying economically useful traits. Altogether, NGS libraries were prepared and sequenced on an Illumina MiSeq platform(Illumina) for 48 samples, for 40 of which it was possible to determine phylogenetic lineages: 28 belonged to haplogroup B, 10 to haplogroup A, and one sample each to haplogroups C and D. Study of the genes associated with economically useful traits revealed the samples with nucleotide substitutions in the MC1R gene leading to black coat color: two samples with c.218T>A, one with c.361G>A, and two with both substitutions simultaneously, as well as one sample with the substitution in the GDF8 gene associated with muscle hypertrophy and one with the substitution in the TYRP1 gene associated with brown coat color. The data obtained confirm a high genetic diversity of sheep from ancient southwestern Siberia and the utility of targeted sequencing for the study of ancient DNA samples.