Isoflavone contents in soybean seeds are affected by both genetic and environmental factors. Correlation analysis between these factors and isoflavone contents are considered as valuable inputs when breeding improved soybean cultivars. In this study, the seeds of 49 soybean accessions grown in Korea were grouped as black, yellow, green, yellowish-green, pale yellow, and green with a black spot based on their seed coat colors. The contents of 12 isoflavones were analyzed and the association between isoflavone content and seed coat color was determined. The accessions were also grouped as early, intermediate, and late-maturing based on their days to maturity. Out of the 12 isoflavones, 11 were found in 2 accessions, 9 in 18 accessions, 8 in 11 accessions, 7 in another 11 accessions, and 6 in 7 accessions. The total isoflavone content (TIC) in black, yellow, green, yellowish-green, pale yellow, and green with black spot soybeans was in the ranges 2.110 ~ 5.777, 2.487 ~ 4.733, 2.185 ~ 4.413, 2.681 ~ 4.065, 1.827 ~ 4.085, and 3.376 ~ 4.133 ㎎/g, respectively. The average TIC was highest in green with black spot soybeans (3.616 ㎎/g), and lowest in pale yellow soybeans (2.875 ㎎/g). Besides, the average TIC was lowest in early maturing accessions compared to late- and intermediate-maturing accessions. TIC was strongly correlated to malonylgenistin (r = 0.91) and malonyldaidzin (r = 0.78) contents, and poorly correlated to glycitein (r = 0.04) and malonylglycitin (r = 0.18) contents. Also, days to maturity showed strong correlation with malonylgenistin (r = 0.47) content and TIC (r = 0.38). The principal component analysis outlined accessions with high TIC and diverse isoflavones along the first and second components, respectively. The results of the present study depicted that green soybeans with a black spot could be sources of high TIC. Furthermore, late-maturing accessions with diverse isoflavones in their seeds could be useful in future agricultural systems in Korea.