Provenance variation and genetic variability in pod and seed traits were carried out with 232 candidate plus trees of Pongamia pinnata collected from selected agro-ecological zones of southern peninsular India during February-March 2008 to 2010. Significant variation (P < 0.01) for pod and seed traits across zones and provenances within zones was recorded. The southern dry and transition zone of Karnataka showed the highest mean value for all the pod and seed traits. A significant negative (P < 0.05) correlation and positive correlation was recorded for latitude with 100-seed weight and seed germination, respectively. Altitude positively correlated with 100-pod weight and negatively correlated with oil content. Phenotypic co-efficient of variation was higher than the genotypic co-efficient of variation indicating the influence of environment. Central dry zone and eastern dry zone of Karnataka showed high heritability and genetic advance for 100-pod weight, 100-seed weight, and seed germination. Positive significant (P < 0.05) genotypic correlation of co-efficient was recorded between seed thickness and oil content (0.211). Germination percentage showed significant positive correlation with seed weight and oil content. Path analysis revealed that seed thickness contributed directly to oil content (0.272). Based on D2 analysis, pongamia accessions could be grouped into seven clusters. Maximum diverse Clusters I and VII were identified based on inter-cluster distance (40.19). Thus on the basis of the present findings, it might be suggested that accessions from these clusters could be most suitably used for hybridization and in situ germplasm conservation.