The ancient Hungarians originated from the Ural region in today's central Russia and migrated across the Eastern European steppe, according to historical sources. The Hungarians conquered the Carpathian Basin 895-907 AD, and admixed with the indigenous communities. Here we present mitochondrial DNA results from three datasets: one from the Avar period (7(th)-9(th) centuries) of the Carpathian Basin (n = 31); one from the Hungarian conquest-period (n = 76); and a completion of the published 10(th)-12(th) century Hungarian-Slavic contact zone dataset by four samples. We compare these mitochondrial DNA hypervariable segment sequences and haplogroup results with published ancient and modern Eurasian data. Whereas the analyzed Avars represents a certain group of the Avar society that shows East and South European genetic characteristics, the Hungarian conquerors' maternal gene pool is a mixture of West Eurasian and Central and North Eurasian elements. Comprehensively analyzing the results, both the linguistically recorded Finno-Ugric roots and historically documented Turkic and Central Asian influxes had possible genetic imprints in the conquerors' genetic composition. Our data allows a complex series of historic and population genetic events before the formation of the medieval population of the Carpathian Basin, and the maternal genetic continuity between 10(th)-12(th) century and modern Hungarians.