The genetic diversity among 11 species of genus Glycine (altogether 37 accessions) was evaluated through SSR analysis. The number of alleles in different loci ranges from 6 to 29, averaging 15.9 per locus; alleles of subgenus soja account for 71.5% of those in subgenus Glycine, and the fingerprinting among subgenus Glycine is more divergent than that of subgenus soja. Principal factor analysis shows that the first and the second principal factor can classify genus Glycine into two groups which represent subgenus Glycine and subgenus soja. The results of UPGMA indicate that G. mas, G. soja and G. gracilis in subgenus soja are different species.