Jatropha curcas L is an economically potential tree species gaining interest globally because of its feasible contribution towards production of commercial biofuel. Little is known however, of its genetic variation patterns within Kenyan accessions for maximum exploitation. Eight populations covering most of its distribution range in Kenya were sampled and leaves of 160 individual trees collected. Analysis of molecular diversity was carried out using random amplified polymorphic DNA (RAPD) markers. Ten random primers generated 251 loci that were scored for diversity. Shannon's diversity index varied from 0.116 (Likoni) to 0.360 (Namanga). Analyses of molecular variance (AMOVA) showed that, more variation (53%; P= 0.01) was partitioned among populations while 47%(P= 0.01) variation was partitioned within populations. Nested analysis of variance showed no variation across regions (0%; P> 0.01). The level of genetic structure and diversity may be explained by the modes of germplasm introductions and the biological traits of J. curcas. Based on these results, Jatropha accessions are quite variable and seeds collected from various populations are bound to exhibit wide variation. Selection of a J. curcas breeding population should encompass a large number of individuals across all accessions in order to capture the wide genetic variation.