The aim of this study was to evaluate the genetic diversity of Jatropha curcas in Chiapas, Mexico using AFLP markers. The AFLP technique allowed us to estimate the genetic relationships in the germplasm of J. curcas and to detect a high level of polymorphism. Analysis of the frequency and distribution of polymorphic fragments allowed us to detect the highest number of rare fragments in one single accession (e.g., accession number 1 from Tuxtla Chico). Besides being an accession that exhibits traits of agronomic importance (such as the presence of 100% pistillated flowers), this diversity of rare fragments may allow for development of markers for identification of this accession and/or development of markers linked to this trait. In addition, very divergent collections have been detected from regions where high average oil content and other characters associated with productivity have been found. Moreover, the analysis of genetic relationships, Analysis of Molecular Variance (AMOVA) and the diversity index (DI = 60%) confirm a broad gene pool in the J. curcas germplasm from Chiapas, Mexico. The high diversity found within the accessions showed non-random mating between groups and/or regions of accessions of J. curcas, which complicates the selection of representative collections. (C) 2011 Elsevier Ltd. All rights reserved.