The aim of this study is to examine the effect of different doses (control, 5, 10, 15, 20 and 25Kr) of gamma irradiation on seed germination, flowering, fruit and seed traits of Jatropha curcas and to identify DNA polymorphism among the mutants through a Randomly Amplified Polymorphic DNA (RAPD) marker analysis. The improved agronomic traits such as flowering, fruits and seeds were recorded in 5Kr dose and seed germination percentage in 10Kr dose treated plants, while corresponding parameters were reduced significantly (P>0.05) in 25Kr dose gamma rays treated plants when compared to that of control. All the twenty-three random primers used except six primers, namely OPAW16, OPAK07, OPAK15, OPS01, OPAK20 and OPAL09 were showed polymorphic bands. The primers: OPAW16, OPAK07, OPAK15, OPS01, OPAK20 and OPAL09 produced only one band each across the six mutants, while the primers: OPU13, OPAB 15, OPF01 and OPAB11 were produced with maximum number of bands (8). The number of amplicons varied from 1 to 8 with an average of 3.9 bands, of which 2.3 were polymorphic. The percentage of polymorphism per primer ranged from 0 to 100 with an average of 55.16%. The Jaccard’s coefficients of dissimilarity varied from 0.324 to 0.397, indicative of the level of genetic variation among the mutants studied. The maximum dissimilarity value (0.397) was observed in 5Kr mutant while the minimum value (0.250) was observed in 20Kr mutant when compared to that of control. In a dendrogram constructed based on genetic similarity coefficients, the mutants were grouped into three main clusters; (a) control, 10, 15 and 20Kr dose mutants clustered together, (b) 25Kr dose grouped alone, (c) 5Kr dose also grouped alone. The mutants showing the differences in morphological traits showed DNA polymorphism in PCR profile amplified by RAPD marker. It is concluded that DNA polymorphism detected by RAPD analysis offered a useful molecular marker for the identification of mutants in gamma radiation treated plants.