Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia

•Three major ethno-linguistic groups in the Republic of North Macedonia were analyzed for 17 Y-SNPs and 27 Y-STRs.•The haplogroup analysis revealed different dominant male ancestral lineages for the three subpopulations.•The combined Y-SNP/Y-STR analyses place the North Macedonians in the genetic landscape of Southeastern Europe.•This study adds high-resolution Y-STR profiles categorized by phylogenetic Y-SNPs from North Macedonia to the YHRD.