Pongamia pinnata has received much attention in recent years as a source of seed oil that can provide a substitute for diesel fuel. Very little molecular work has been reported on this species. This paper reports our studies on the diversity amongst the CPTs (candidate plus trees) of P. pinnata previously identified on the basis of morphometric traits, particularly pod and seed traits. For this RAPD (random amplified polymorphic DNA) markers were used to determine the genetic diversity among 10 genotypes of P. pinnata CPTs selected for suitability for energy production. For further investigation, 18 primers generating stable band patterns from 40 tested arbitrary primers were selected. A total of 210 amplification products were obtained of which 10.48% were polymorphic. The genetic similarity index ranged from 0.11 to 0.87. Genetic distance values were used to generate a dendrogram (UPGMA) between the genotypes. The Mantel method used for comparing the similarity matrixes produced correlation coefficients that were statistically significant for the RAPD marker. This genomic analysis allows a cost effective characterization of CPTs of P. pinnata. The present investigation supports in future the development of genetic map in Pongamia which are a highly useful tool in breeding and may provide information on the inheritance of features crucial for increase seed yield, oil content and the resistance to key insects and pests. Thus this study warrants Pongamia producers to realize its full potential and contributes for its sustainable production and improvement. (C) 2011 Elsevier Ltd. All rights reserved.