Soybean (Glycine max, 2n = 2x = 40) is broadly distributed throughout East and South East Asia, and important crop as a source of protein, oil, food and animal feed. In order to better understand the morphological differentiation of soybean germplasm collected from China, Japan, Korea, Philippines, America, we analyzed the morphological variabilities among 629 soybeans with 11 morphological traits, such as growth type, leaflet, flower color, trichome, seed coat color, color inside seed etc. and measured the fatty acid composition. The result of the principal coordinates analysis (PCoA) based on the 11 morphological traits revealed diversity among all accessions. The PCoA separated the accessions into two main groups, each group with distinctive features. Among tested germplasm, the contents of five fatty acids were as follows: linolenic acid (2.8%-16.23%), linoleic acid (27.4%-56.6%), oleic acid (9.2%-35.0%), stearic acid (2.9%-8.8%), and palmitic acid (8.7%-17.1%). The fatty acid composition has not shown significant variation among all accessions. IT 22268 was the highest linolenic acid composition (16.2%), while IT 154687 was the lowest (2.8%). Forty three of 629 accessions showed the arachidic acid (0.5%-3.6%), which is the saturated fatty acid with a 20 carbon chain and is as a minor constituent of peanut oil (1.1%-1.7%). This result of this characterization served as reliable resources for detailed description and new functional plant breeding of soybean varieties.