In the present study we evaluated the applicability for forensic and evolutionary studies of 21 Y-STR loci (DYS437, DYS447, DYS448, DYS449, DYS456, DYS481, DYS504, DYS510, DYS518, DYS532, DYS536, DYS542, DYS552, DYS562, DYS576, DYS587, DYS612, DYS626, DYS644, DYS710, and Y-GATA-H4). Allele sequence analysis, allele diversity, gene diversity, allele frequency spectrum, discrimination capacity and informativeness for assignment were studied in European English, Asian Indian and Xhosa population groups sampled in South Africa.Seven loci showed size homoplasy. Individuals with mixed ancestry were identified using a statistical method for population assignment and a phylogenetic network. In comparison to our previous minimal haplotype data for the same population groups these loci showed significant increase in discrimination capacity (overall, from 0.773 to 0.958).