The total and individual phenolic profiles and their contribution to antioxidant capacities of seed coats and dehulled beans of black and yellow soybeans were investigated. In addition, lipoxygenase (LOX) and peroxidase (POD) activities were also determined. Black seed coats had the highest content of total phenols, flavonoids and anthocyanins, in addition the highest catechin and protocatechin contents. On the other hand, dehulled beans from yellow soybeans had the highest levels of ferulic and p-coumaric acid content, and free and bound isoflavone content. The LOX activity was concentrated in the dehulled beans of both black and yellow soybeans, while a high POD activity that can be attributed to a dominant gene EpEp was presented in seed coats of yellow soybean genotype Galeb. Due to the high concentration of phenols, the black seed coats from soybean genotypes Black Tokio and Cornaja had the highest ABTS(center dot+)-scavenging capacity (597.46 and 486.15 mmol Trolox Eq./kg d.m., respectively). The results suggest that the black seed coat as well as dehulled bean from yellow soybeans would potentially provide sources of natural antioxidants that may play a crucial role in human health protection.