Introduction: The Simarouba species is considered one of the promising feedstock for biodiesel producers as the seeds have high oil content and are non edible. These species can be grown well even in wasteland. As Simarouba is polygamodioecious in nature and have a long juvenile period assessment of genetic variability in Simarouba germplasm is essential for exploitation of genetic resource for plant improvement programs. Objective: The present investigation aims to find the genetic diversity of male, female and andramonieocus Simarouba species using RAPD markers. Methods: Fifty Random amplified polymorphic DNA primers were used for genetic analysis of male, female and hermaphrodite Simarouba species. The binary data obtained from the RAPD banding profile were analysed using Wards Squared Euclidean distance and construct dendogram through UPGMA (Unweighted Pair Group Method with Arithmetic average statestica). Jac card similarity coefficient was constructed using NTSYS ( Numerical Taxonomy System, PC version 2.02e programme to determine genetic relation among Simaroba individuals. Results: RAPD primers yielded 223 amplicons of which 176 (78.92 % ) were polymorphic. An average number of bands per polymorphic primer observed is 4.46. Jaccard Similarity Matrix between male, female and hermaphrodite Simarouba genotypes varied from 0.06 to 0.81. Among the various combinations, maximum similarity of 81 % was observed between Female and hermaphrodite individuals. While maximum dissimilarity of 63 % was found between female and male individuals. Dendrogram generated by UPGMA (Unweighted Pair Method with Arithmetic Mean ) grouped female and male plants in separate groups. Conclusion: Molecular markers employed in this investigation showed genetic diversity between crop genotypes. This study provides development of strategies for genetic analysis and crop improvement in Simarouba species.