Soybean seeds are one of the best sources of plant-based high-quality proteins and oils. The contents of these metabolites are affected by both environmental and genetic factors. In this study, 49 soybean germplasms were cultivated in Korea, the contents of total protein, total oil and five fatty acids were determined, and the influences of seed coat color and seed weight on each were assessed. The total protein and total oil contents were evaluated using Kjeldahl and Soxhlet methods and were in the ranges of 36.28-44.19% and 13.45-19.20%, respectively. Moreover, the contents of individual fatty acids were determined as area percentage from acquired gas-chromatography peaks. The contents of palmitic, stearic, oleic, linoleic and linolenic acids were in the ranges of 9.90-12.55, 2.45-4.00, 14.97-38.74, 43.22-60.26, and 5.37-12.33%, respectively and each significantly varied between the soybean germplasms. Unlike total oil and fatty acid contents, total protein content was not significantly affected by both seed coat color and seed weight. Cluster analysis grouped the soybeans into two classes with notable content differences. Fatty acids were the main factors for the variabilities seen between the soybean germplasms as observed in the principal component analysis. Correlation analysis revealed a significant but negative association between total oil and total protein contents (r = -0.714, p < 0.0001). Besides, a trade-off relationship was observed between oleic acid and linoleic acid (r = -0.936, p < 0.0001) which was reflected with respect to both seed coat color and seed weight. Among all colored soybeans, pale-yellow soybeans had the highest and the lowest levels of oleic acid and linoleic acid, respectively each being significantly different from the rest of colored soybeans (p < 0.05). Likewise, oleic acid content increased with seed weight while that of linoleic acid decreased with seed weight (p < 0.05). In general, this study showed the significance of seed coat color and seed weight to discriminate soybean genotypes, mainly in terms of their fatty acid contents. Moreover, the soybean germplasms with distinct characters and fatty acid contents identified in this study could be important genetic resources for cultivar development.