•ISSR detected medium to high variability in the evaluated full-sib families of J. curcas.•UPGMA dendrogram grouped all the accessions into four clusters.•The 108 full-sib accessions of the Jatropha curcas showed a mean distance of 61%.•Most of the genetic variations existed within families and family 1 is the most divergent. The aim of this study was to evaluate the genetic diversity between and within of six full-sib families of Jatropha through ISSR molecular markers. Six genitors were selected based on oil and seed potentiality. A set of 20 ISSR markers was used. The genetic distances were estimated based on Jaccard similarity coefficient and the descriptive statistics of populations for estimation of genetic parameters were also performed. A total of 177 polymorphic bands were obtained. The polymorphism within full-sib families ranged from 22 to 51.6% for families 2 and 5, respectively. The similarity analysis between families presented an average distance of 61%. The effective number of alleles varied from 0.56 to 1.86. The lowest value for Nei’s gene diversity index was 0.34 and the largest was 0.46 and the Shannon information index ranged from 0.51 to 0.65. The genetic variability analysis, by ISSR molecular markers showed low genetic dissimilarity within of full-sib families of Jatropha. However, the evaluation between the full-sib families demonstrated that the accessions belonging to family 1 are the most divergent, and should be considered in future artificial hybridations strategies.