The Japanese rose bitterling, Rhodeus ocellatus kurumeus, is an endangered cyprinid species. The main reason of drastic diminution of R. o. kurumeus has been suggested to be due to hybridization between this subspecies and R. o. ocellatus introduced from China. Both RFLP analysis of mitochondrial DNA and RAPD-PCR analysis of genomic DNA were performed to elucidate the genetic introgression of R. o. ocellatus into R. o. kurumeus. The two subspecies were distinguished in the D-loop region of mtDNA by six restriction endonucleases. Rhodeus o. kurumeus had eleven subspecies-specific RAPD markers and R. o. ocellatus had two. Except some R. o. kurumeus populations, most of the populations of R. ocellatus in Japan were hybrids, equipped with subspecies-specific RAPD markers for the two subspecies, respectively. The genetic constitution of these markers in hybrids, however, greatly differed among populations. The R. o. ocellatus mtDNA was predominantly observed in hybrid populations, except two populations with mtDNAs of the two subspecies. Judging from the genetic dominance of morphological and physiological characters of R. o. ocellatus against R. o. kurumeus, hybrids probably have the same ecological dominance as R. o. ocellatus against R. o. kurumeus. Therefore, it is considered that R. o. kurumeus not only has its genetic property spoiled by hybridization with R. o. ocellatus, but also is expelled by R. o. ocellatus and hybrids. The replacement of mtDNA and genomes of R. o. kurumeus with those of R. o. ocellatus in hybridization might be accelerated by the backcross between hybrids and R. o. ocellatus.