Genetic variability in the wild genotypes of Jatropha curcas L., collected from different parts of Northeast India, was analyzed using two different single primer amplification reactions (SPAR) methods, viz., inter-simple sequence repeats (ISSR) and directed amplification of minisatellite DNA (DAMD). A total of 36 genotypes were used to investigate the existing natural genetic variation at intra-specific level. One hundred forty nine (149) amplification products were scored by ISSR and DAMD, both of which collectively showed 75.83% polymorphism with a mean intra-population genetic diversity (H-s) of 0.1309. However, their level of diversity at inter- and intra-population levels was significant, with the percentage of polymorphic loci (P) ranging from 22.82% to 44.30%, Shannon's information index (H-pop) from 0.1302 to 0.2541 and Nei's gene diversity (H-E) from 0.0831 to 0.1723 with mean Nei's gene diversity (H-T) 0.2202 and the overall estimate of gene flow being (Nm) 0.8085. Analysis of molecular variance (AMOVA) showed that 68.88% of variation at intrapopulation level, whereas 31.12% variation was recorded at inter-population level. Cluster analysis also supported the existence of genetic diversity in the genotypes of J. curcas collected from Assam and Meghalaya provinces of Northeast India. Present investigation suggests the efficiency of SPAR methods to estimate the genetic diversity precisely which can define genetic relationship and population genetics of]. curcas. (C) 2011 Elsevier Ltd. All rights reserved.