The maternal gene pool of Csangos, Szeklers and “average” Hungarians can be descended from 10th–12th century ancient Hungarians, and the differences in their haplogroup composition from the conquerors can be explained by genetic drift (Supplementary Table S7). It is an interesting phenomenon that some Asian haplogroups (A, B, C, G2a) that occured in the conquerors also occurred among Szeklers. This could suggest a sizeable legacy of the conquerors or it may mean that these Asian influences reached Romania in other time periods. Of the 76 detected conqueror haplotypes, 21 had matches in the modern Szekler and Hungarian populations (11.2–15.4% of all lineage types), but none were Asian (Supplementary Table S11). Fourteen conqueror lineages had matches in the Csango dataset, which represents a greater proportion (22.6%) of the total number of Csango lineage types, one of which belonged to the Asian C haplogroup. We would need more medieval samples from Romania and a reconsidered sampling of the current population in the Carpathian Basin in order to better estimate the genetic relations among past and present populations.