Understanding plant morphological and seed characteristics is an essential step for the utilization of genetic resources to improve targeted traits in soybean breeding programs. The purpose of this study was to evaluate the agronomic traits and seed pigments of 469 black soybean germplasms with green cotyledons to identify useful resources using multivariate analyses, correlation, principal component analysis (PCA), and cluster analyses. The results showed that the range of flowering days from planting were 37.7-71.5 days, harvesting days from planting were 112.3-153.0 days, plant height was 49.6-151.6 cm, and 100-seed weight was 9.1-49.3 g. According to the correlation analyses with agronomic traits, flowering and harvesting days were positively correlated with the plant height, number of nodes, and number of branches. Additionally, it was found that the chlorophyll a and total chlorophyll content had the greatest effect on the green color of the cotyledon. Based on the PCA, 13 quantitative traits were compressed into three components. The first three principal components accounted for 82.5% of the total variance. In this study, black soybean germplasms with green cotyledons were divided into four clusters by the K-means cluster analysis (non-hierarchical procedure), based on the PCA. The cluster analysis showed that chlorophyll a and plant height had a significant effect on the clustering of the black soybean germplasms used in this study. This study provides opportunities to easily select useful genetic resources for the development of new black soybean cultivars.