Moringa oleifera is potentially an economically important tree species. It has gained interest globally for its multipurpose uses, in particular as a source of nutrition and oil, as well as for its various medicinal properties. Moringa is native to India, Malaysia and the Middle East, but have been introduced to many countries throughout Africa. There is however limited knowledge regarding the genetic variation of both native and introduced populations of Moringa, although phenotypic observations suggest the presence of significant genetic diversity. To do this we used Moringa collections from different locations including India, South Africa and Hawaii, with different cultivars present in the foreign samples. Molecular markers such as Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR) were evaluated for their efficiency as a marker system in Moringa, based on their success in other tropical tree population studies. The comparative analysis between the two revealed that both marker systems identified similar heterogeneity of 0.438 (RAPD) and 0.481 (SSR). However, the microsatellite marker was more effective for assessing genetic diversity, with a marker index (MI) value of 5.77 compared to 2.96 (RAPD), within our data set. Three major groups among the 71 accessions were clustered together in the dendogram and Principle Co-ordinate Analysis (PCoA), based on the genetic similarity matrices generated by both markers. Both cultivars were grouped together irrespective of origins, suggesting a relationship of genetic identity rather than geographical origins. The markers investigated in this study were found to be effective for determining genetic diversity, verifying higher genetic variation among the S.A. accessions of Moringas and distinguishing them from the cultivars investigated. This information could possibly be exploited for cultivar development in tree improvement programmes.