We typed the mtDNA of 111 medieval individuals and performed population genetic and statistical analyses, focusing on three populations that existed in the 7th–12th centuries in the Carpathian Basin. The earliest population under study is the 7th–8th century Avars from the southern part of modern Hungary (Fig. 1). The genetic results from the Avars demonstrate their predominant southern and eastern European maternal genetic composition, with some Asian elements. The local continuity of the Avar population on the southern Great Hungarian Plain to the Hungarian conquest-period cannot be rejected by haplogroup based simulation analyses (TPC, Supplementary Table S7) and was also demonstrated on PCA plots (Fig. 3a, Supplementary Fig. S1). However, sequence-based tests and shared haplotype analyses showed a low level of identical maternal lineage among the Avars and ancient Hungarians, even when including the geographically connecting southeastern group of the conquerors in the calculations (Fig. 5, Supplementary Table S10). The Avar dataset originates from a single micro regional group of the complex Avar society, who buried their dead in catacomb graves. Furthermore, anthropological results showed that this part of the Avar population represents mostly Europid, local morphological characters, and therefore it cannot be used as a proxy of the whole Avar population of the Carpathian Basin. Further regional groups should be analyzed from the late Avar period for a better estimation of the Avar-Hungarian continuity.