RFLPs of chloroplast (cp) and mitochondrial (mt) DNA have been used to characterize the cytoplasmic genome of wild soybean, Glycine soja, growing in China. We have found from the RFLPs of that the cytoplasmic genomes of most Chinese wild soybeans have a combination of cpIII with mt-a or a combination of cpII with mt-b accompanied by mtIV or mtV according to our classification. CpII was not observed in combination with mt-a and cpIII was not observed in combination with mt-b. The regional distribution of these two types showed clines with opposite directions. The Yangtze River Valley had the greatest diversity in each of cp and two mt profiles detected in this study and the cytoplasmic genome combining these three profiles showed the highest degree of polymorphism in this region. The Yangtze River Valley may be a center of cytoplasmic diversity of wild soybean and may contain various genetic resources of soybean.