In order to examine genetic introgression from the orange-red type commercial strain of Oryzias latipes (himedaka) to wild medaka populations, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome b gene was conducted for 45 populations from the Yamato River system, Nara Prefecture and two fish farm populations from special product grounds of himedaka (Yamatokoriyama and Yatomi Cities). Orange-red type fish only were collected from three sites, and a mixture of wild and orange-red types from sympatric populations at four other sites in theYamato R. system. Most orange-red type specimens had the B27 mitotype, being identical with that of the typical orange-red type Hd-rR strain. Although most of the wild type fish individuals had mitotype B1a, inferred as one of the native mitotypes in the Yamato R., four from three sites had mitotype B27, implying genetic introgression from himedaka to wild medaka populations.