Genetic identification is at the base of parental selection in varietal development programs. Agronomic and photosynthetic characters and sequence-related amplified polymorphism (SRAP) markers were analyzed for two legume species which included 23 mungbean (Vigna radiata (L.) Wilczek) and four blackgram (Vigna mungo (L.) Hepper) genotypes. The results revealed that the seeds/pod, plant height, pods/plant, pod length, days to flowering, and all photosynthetic characters studied had a significant correlation with the yield/plant. Using UPGMA analysis with phenotypic data, five clusters and two individuals were identified. Twenty-five SRAP primer combinations generated 562 amplified bands, of which 507 were polymorphic (90.2%). The average numbers of scorable and polymorphic bands/primer pair were 22 and 20, respectively. Two major clusters coincided with two species having a 100% bootstrap value. Within the mungbean cluster, there were two subclusters containing 12 and 11 mungbean genotypes. Mantel’s test demonstrated that the polymorphisms given by SRAPs were associated with agronomic and photosynthetic variability (r = 0.734, p < 0.01). These results allow promising mungbean genotypes to be identified through genetic diversity and field performance which can be utilized as potential parents towards future breeding programs. Moreover, the factors which contribute most to yield/plant can be simultaneously used as selection criteria for yield improvement.