Restriction fragment length polymorphisms (RFLPs) of chloroplast and mitochondrial DNAs of various soybean landraces and wild soybeans collected in China and Japan were analyzed to characterize their cytoplasmic genome and to consider the polymorphism and phylogeny of soybean from the maternal lineage. Three chloroplast and 6 mitochondrial types were distinguished and, in their combinations, 8 cytoplasmic genome types were detected in specimens of soybean landraces collected from China and Japan. The cytoplasmic genome diversity was higher in China, especially in the Yangtze River Valley. The main group of soybean landraces including current cytoplasmic types was composed of the 5 cytoplasmic types which were related phylogenetically to each other and were considered to occur mainly in the Yangtze River Valley of China, though one of them seemed to have differentiated in Japan. Three unique types of soybean cytoplasmic genome were markedly different in the genome constitution from each other, and considered to be derived separately from wild soybean with the same cytoplasmic genome and to have occurred independently in remote regions, i.e. the northern region and the Yangtze River Valley of China and the southern and northern regions of Japan, respectively. Based on the constitution of the cytoplasmic genome, it is suggested that domestication of soybean may have possibly occurred in various areas and shows multiple origins.