The 101 ancient Hungarian samples belong to 75 HVS-I haplotypes (haplotype diversity Hd = 0.987). The haplotype diversity is highest in the Avar group, and lowest in the contact zone dataset (Table 1). The shared haplotype analysis (SHA) shows that medieval populations from Southern Europe (Spain and Italy) shared over 50% of haplotypes with the conqueror population (Fig. 5 and Supplementary Table S10). High proportions of shared lineages with the conquerors were detected in the contact zone population (43.5%), Vikings from Norway (39.3%), Iceland (39.7%), and 6th-century Lombards in Hungary (39.3%). The SHA analysis was strongly influenced by altering haplotype diversity and the high number of Cambridge Reference Sequence (rCRS) H lineages in medieval Spanish, Italian and Norwegian Viking groups, which caused high proportion of lineage sharing with only a small number (n = 4–5) of shared lineage types. Medieval populations from Italy and Spain shared many of their haplotypes (40–48%) with the Avar and contact zone populations as well. On the other hand, many lineages of the Bronze Age Andronovo, Baraba, and Bronze Age population of the region of today’s Kazakhstan were shared with the conquerors (37.5–29.4%), with some identical Asian lineages among them.