Crop wild relatives are important components of agro-ecosystems as potential gene contributors for crop improvement programmes. Cajanus scarabaeoides (L.) Thou., a pigeonpea wild relative is crossable with cultivated pigeonpea and possesses several beneficial traits. Hundred accessions conserved at the ICRISAT genebank were characterized for 13 quantitative and ten qualitative traits to assess the diversity in the collection. Highly significant genotypic variance for leaflet length, days to 5% maturity, seeds per pod, 100-seed weight, seed protein content and trichome density and length was observed. All C. scarabaeoides accessions used in the present study are the best sources for extra early ( < 80 d to 50% flowering) and early maturity (80–100 d to 50% flowering). Eight accessions (ICP 15692, ICP 15696, ICP 15698, ICP 15699, ICP 15712, ICP 15719, ICP 15732 and ICP 15758) and the control ICP 15695 have produced more than 92% healthy pods per plant and higher number of seed per pod (4–6 seeds). Accessions in cluster 2, 3 and 4 with low mean values for days to 50% flowering were found as the best sources for early flowering and maturity. Accessions in cluster 2 and 3 for seeds per pod and cluster 2 for healthy pods per plant were found as promising sources for use in crop improvement. Mean diversity over all clusters was highest (H= 0.57 ± 0.01) for seeds per pod and lowest for days to 50% flowering (0.48 ± 0.02). Significant negative correlation between pods per raceme and healthy pods per plant ( − 0.213) indicated high pod damage in racemes having more pods. Trichome length had highly significant negative association with healthy pods per plant ( − 0.293). The probability map generated using FloraMap, a GIS tool, revealed the occurrence of C. scarabaeoides quite close to the origin and dispersal of pigeonpea. The probability (>75%) map identified a total of 118 provinces covering 790 districts in Bangladesh, Cambodia, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Thailand and Vietnam as geographical gaps in the collection. Complete passport data including location coordinates should be collected while collecting the germplasm to analyze the spatial aspects of species distribution.