Abstract: Background and Objective: M. oleifera belonging to the monogeneric family Moringaceae. It is drought-tolerant and must be cut back several times to make it branch out more. It tolerates a large range of soils and rainfall conditions. The present study has been aimed to estimate genetic relatedness among the seeds of M. oleifera from 3 different states of India i.e., Himachal Pradesh, Maharashtra and Uttarakhand using RAPD markers. Materials and Methods: Estimation of genetic relatedness among the seeds done through Isolation of genomic DNA, agarose gel electrophoresis, polymerase chain reaction (PCR) amplification by using RAPD (OPA, TC series) primers and UPGMA dendrogram. Results: Initially, nine random decamer primers were used in the study and based on the higher degree of polymorphism obtained only 4 primers were selected for further study which generated reproducible RAPD patterns. The number of bands in the amplified products for different samples which resulted from the selected RAPD primers varied between 40-50, where the size range of various amplicons for different samples varied from 202-3010 bp, approximately. Clustering based on RAPD fingerprints data revealed that the samples from different district of Himachal Pradesh (HP1B and HP2M), Uttarakhand (UK1D and UK2N) and Maharashtra (MH1L and MH2P) got paired into three separate clades at similarity level of 88.5%, showing maximum homology within their respective pairs. Conclusion: The results suggest that, high level of polymorphism was observed between the samples from south-central and northern parts of the country which showed that they were distantly related to each other.