Thirty four Jatropha germplasm accessions, selected based on unique phenotypic traits from 180 accessions collected from diverse geographical regions were subjected to field evaluation and molecular analysis. The field evaluation using eight quantitative traits showed significant variation among the germplasm. The molecular analysis using 56 RAPD and 40 ISSR primers resulted in 7 and 8 clusters, respectively. The accession lC541633 from Bastar (Chattisgarh) emerged as the most diverse accession. An attempt has been made to correlate the clustering based on molecular data with the quantitative traits. There was partial correlation between the quantitative traits and molecular data. Interestingly, the diverse accessions according to molecular diversity were characterized by unique phenotypes. Time of flowering, inflorescence type and number, leaf colour and texture were the traits contributing to variation. These traits may be used in identification of diverse accessions during germplasm exploration surveys or short listing of accessions for crossing in Jatropha improvement programmes. (C) 2010 Elsevier Ltd. All rights reserved.