Morphological characterization of 20 common millet (Panicum miliaceum L., 2n = 4x = 36) cultivars and landraces revealed four distinct clusters which were apparently consistent with the grain colors of black, black and brown, red, yellow, and white. Seed remains of medieval millet, recovered from a 15th century layer (King's Palace, Budapest, Hungary), showed reddish yellow grain color after rehydrating on tissue culture medium that was close to grain color of modern cultivar Omszkoje. aDNA of medieval commom millet was extracted successfully, analyzed and compared to modern common millets by ISSR, SSR, CAP and mtDNA. Analyses of fragments and sequences revealed polymorphism at seven ISSR loci (15 alleles) and at the 5S-18S rDNA locus of mtDNA. CAP analysis of the 5S-18S rDNA fragment revealed no SNPs in the restriction sites of six endonucleases TaqI, BsuRI, HinfI, MboI, AluI and RsaI. Sequence alignments of the restriction fragments RsaI also revealed consensus sequence in the medieval sample compared to a modern variety. An attempted phenotype reconstruction indicated that medieval common millet showed the closest morphological similarity to modern millet cultivar Omszkoje.