An extensive germplasm exploration survey was undertaken and identified 25 high yielding accessions of Jatropa curcus from different locations of latitudinal and longitudinal spread between 920 and 940 E longitude and 60 to 140 N latitude of the A & N Islands. The genetic diversity among 25 accessions were analysed by using 15 polymerase chain reaction (PCR) markers (07 random amplified polymorphic DNAs (RAPDs) and 08 inter simple sequence repeats (ISSRs). The amplification of genomic DNA of the 25 genotypes by using RAPD analysis has yielded 61 fragments per primer. Number of amplified fragment ranged from two (OPA13) to seven (OPT18). Percentage of polymorphism ranged from 28 .6 % (OPA 13) to maximum of 77.7 %( OPA02). The resolution power ranged from a minimum of 1.20 (OPA13) to maximum of 3.65(OPT 18).Eight ISSR primers generated reproducible amplification of 46 bands across 25 genotypes, of which 26 were polymorphic. The number of amplified fragment ranging from zero (0) to six (12, 13), with an average of 3.25 polymorphic fragment per primer. Percentage of polymorphism ranged from 0 % to a maximum of 100 % (12, 13, and 14). The UPGMA method was used to construct dendrogram and grouped the 25 accessions in six main clusters. Clustering of genotype within groups was not similar between RAPD and ISSR derived dendrogram. The result of the present study shows that J.curcus germplasm within A &N Islands possess diversity up to 55 %.