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The tropical legume Mucuna pruriens(L.) DC. is one of the protein-rich crops well suited for the arid regions of the world, which suffers from low soil fertility and protein-energy malnutrition. Though thought to have originated in Southern China or Eastern India, which includes parts of Northeast (NE) India, the genetic diversity of M. pruriensfrom this region is poorly documented. In this study, we used 25 species-specific genic-microsatellite markers to investigate the diversity and population structure of sixty (60) M. pruriensaccessions from Northeast India alongside assessing variability for the six seed-based economic traits. The study revealed high genetic diversity (I= 0.496), poor population differentiation (GST = 0.038 and FST = 0.061), extensive gene flow (Nm = 7.48), and admixture genotypes in addition to good variability for the seed-based economic traits. These findings will provide a strong basis for future studies on association mapping in addition to broadening the germplasm base for breeding programs in this lesser-known legume crop.