Modern-day Hungarians were very similar to their surrounding Central European populations from the maternal genetic point of view, as demonstrated by previous mtDNA studies1219. In our analyses, the Hungarian speaking Szekler, Ghimes, and Csango minorities in today’s Romania showed differing genetic connections from each other. Whereas the Szekler population was consistent with the Central and Eastern European maternal genetic diversity, the haplogroup and haplotype composition of the Csangos was more related to Near Eastern populations (Supplementary Fig. S4, Table S9). These results correspond to the fact that the Csangos, in the Romanian Ghimes region, are a genetically isolated population20, living separately from both Romanians and Szeklers.