The genetic diversity of 5 populations of Jatropha curcas L. (Euphorbiaceae), a species cultivated in tropical countries and used in biodiesel production, was analyzed by amplified fragment length polymorphism (AFLP). Plants from distinct populations found in the State of Sao Paulo, Brazil, had their genetic diversity characterized by using three primer combinations. The number of polymorphic bands obtained reached 184 and the base pair length of bands ranged from 75 to 350, with average PIC values of 0.418. Accessions from the Aguas de Santa Barbara population presented the highest percentage of polymorphic loci (89.76%), followed by the populations of Catanduva (84.24%), Jales (80.98%), Juruce (78.80%) and Taquaritinga (70.65%). Plants collected from the populations of Taquaritinga and Jales presented the smallest and highest genetic diversities, respectively, measured by using both Nei's genetic variability index (h = 0.2242 and 0.2973) and Shannon's index (I = 0.3359 and 0.4319). The results obtained indicated that 73.1% of genetic variability corresponds to intrapopulational variation and 26.8% to variation among populations. The clustering dendrogram using Jacquard showed four clusters. Three clusters with low genetic diversity grouped most of individuals collected in distinct regions (63.3% JU, 47.0% JA and 82.5% TA) and the fourth with the higher genetic diversity was composed with basically individuals collected in CA and AS, but it also had samples collected in JU, JA and TA, where it is possible to select individuals to be included in breeding programs. (C) 2015 Elsevier Ltd. All rights reserved.