species exhibit a paternal chloroplast inheritance and a maternal mitochondrial inheritance. The levels and patterns of cpDNA and mtDNA introgression between the two pine species, P. pumila and P. parviflora var. pentaphylla, were examined at three mountain sites in Japan. The pine species were examined by using PCR-based diagnostic genetic markers of cpDNA and mtDNA. The survey which was carried out in multiple hybrid zones demonstrated a generality in the uni-directional pattern of cytoplasmic gene flow between the two pine species, i.e. paternal cpDNA flowed from P. parviflora var. pentaphylla to P. pumila, and in contrast, maternal mtDNA flowed from P. pumila to P. parviflora var. pentaphylla. Whenever plants which had a non-native combination of cpDNA and mtDNA were observed, they always had the cpDNA haplotype of P. parviflora var. pentaphylla and the mtDNA haplotype of P. pumila. The existence of only this type of cytoplasmic chimera may suggest that F1 hybrids are successfully produced only in the crossing of P. pumila as the maternal parent and P. parviflora var. pentaphylla as the paternal parent. The present study also detected extensive mtDNA capture in populations of P. parviflora var. pentaphylla located in the southern and middle parts of the Ohu Mountains, Tohoku, Japan. In that area, nearly all of the plants examined had the mtDNA haplotype of P. pumila. The extensive mtDNA introgression suggests that seed flow could be an effective medium for interspecific gene exchange.