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Not AvailableJatropha curcas has gained popularity as a potential biofuel crop but the major constraint for improvement of the crop for yield and seed quality traits is the narrow genetic base of the germplasm. Genetic background of 72 J. curcas accessions representing 13 countries has been elucidated using molecular analysis and biochemical traits. Seed kernel protein, oil content, ash content and phorbol esters revealed variation with accessions from Mexico containing low levels of phorbol esters. Molecular characterization disclosed polymorphism of 61.8 and 35.5% with RAPD and ISSR primers, respectively and Mantel test revealed positive correlation between the two marker systems. Dendrogram based on pairwise genetic similarities and three-dimensional principal coordinate analysis using data from RAPD and ISSR marker systems showed close clustering of accessions from all countries and grouped the Mexican accessions separately in clusters III, IV, V and VI. Presence of the toxic phorbol esters is a major concern and analysis of 28 Mexican accessions resulted in identification of molecular markers associated with high and low phorbol ester content. The identified RAPD and ISSR markers were converted to SCARs for increasing the reliability and use in marker assisted programmes aimed at development of accessions with reduced toxicity. Twelve microsatellite primers differentiated the non-toxic Mexican accessions and disclosed novel alleles in Mexican germplasm. Amplification with primers specific to the curcin coding sequence and promoter region of ribosome-inactivating protein (RIP) revealed polymorphism with one primer specific to RIP promoter region specifically in accessions with low phorbol ester levels. Narrow genetic variation among accessions from different regions of the world and rich diversity among Mexican genotypes in terms of phorbol ester content and distinct molecular profiles indicates the need for exploitation of germplasm from Mexico in J. curcas breeding programmesNot Availabl