Genetic variation in thirty-eight soybean genotypes inculding cultivating (Glycine max) and wild soybeans (G. soja) was analyzed with isozyme and RAPD techniques. The overall genetic variation among the wild soybean was greater and wider than that of cultivating soybeans. The genetic similarity among the studied soybean genotypes was ranged from 0.794 to 0.891 and averaged at 0.8921. In the cluster analysis, wild germplasm was separated from the cultivating germplasm at 83% similarity level. As well, the intermediate type soybeans (G. gracilis) in their morphological appearances were clustered in between cultivating soybeans and wild soybeans. This is the first report on the cluster analysis using molecular genetical approaches in the three types of soybeans.