Amplified fragment length polymorphism (AFLP) fluorescence primers were used to characterize the genetic variation among 63 populations of Jatropha curcas from 10 countries in Asia, Africa and Mexico grown in provenance trials in China and Vietnam. Four primer combinations were used to generate a total of 89 bands of which 87 were polymorphic. Total genetic diversity (Ht) was low (0.15). AMOVA partitioned 31% of variability among populations and 69% within populations. Gene flow (Nm) was found to be low, 0.44, suggesting limited gene exchange among populations. Polymorphic loci (Np = 16), the percentage of polymorphic loci (Pp = 18%), Nei's diversity index (H = 0.07) and Shannon's information index (I = 0.10) all indicated low genetic diversity among populations. The populations from Mexico were exceptional as they all displayed high genetic diversity. The UPGMA-based dendrogram, with corroborative indications from Principal Coordinates Analysis, divided the populations into 4 major clusters. Subpopulations from a wide geographic range within India formed a major cluster suggesting a common origin for these subpopulations; the same was indicated for many of the Chinese subpopulations. Material from a wide range of countries in Southeast Asia and accessions from Africa formed another cluster. The Mexican populations formed a fourth, separate group, relatively distant from the other three clusters, indicating that the Asian material probably does not originate from Mexico. Despite generally low genetic diversity of cultivated Jatropha curcas in Asia, this study identified 6 Asian populations with genetic diversity considerably higher than overall population mean. Though the impact of inbreeding on jatropha fitness is not yet well-understood, it is probable that broadening the genetic base will benefit breeding programs in Asia, guarding against inbreeding depression and providing a range of material with the genetic diversity to adapt to a wide range of planting sites. Drawing from the more-diverse populations identified in Asia as well as from wild material originating in Mexico and other parts of the natural range would be a sound strategy when applied in concert with further research on the species' breeding system, quantitative trait variation and environmental plasticity. (C) 2011 Elsevier Ltd. All rights reserved.