Two hundred wild soybean lines were used to investigate water imbibition of seeds and its relationships with seed coat structure. Those structures were observed under the light microscope and the surface structure and cell arrangement was done under the scanning electron microscope. One hundred and ninety seven out of 200 wild soybean genotypes (98.5%) had hard seed and only three wild soybean genotypes, YWS16, YWS67, and YWS136 collected in Korea showed the permeability to water. Those three permeable lines showed less endocarp deposits whereas the hard seed lines did thick deposits. Larger cracks were found in permeable seed lines, however, no crack or tightly cracks were found in hard seed lines. The structure in the cell arrangement of palisade layer was looser than hard seed lines. The less compact cell arrangement in palisade cell layer and lower endocarp deposits with large cracks were considered as main factors affecting the permeability of wild soybean seeds.