Molecular linkage maps provide a powerful tool for the analysis of plant genome structure and function including the detection of quantitative trait loci (QTL). The molecular linkage map of soybean was constructed using an 88-individual RIL population derived from a cross between cultivated Changnong 4 and semi-wild Xinmin 6. The map contains 22 linkage groups and 240 markers, including 100 RFLP, 33 SSR, 62 RAPD, 42 AFLP, 1 SCAR and 2 morphological markers. It covers approximately 3,713.5 cM of soybean genome. Analysis of 72 RFLP markers showed that 16 of them revealed two or more independent loci and it suggested that there is an extensive homologous region in soybean genome. This map compared very well with the other published soybean maps.