Natural vanilla (Vanilla planifolia G. Jackson, syn. V. fragrans) is native to the tropic forest of Mexico. It is now cultivated in humid tropical areas of Africa, America, Asia and Australia continents. In Tanzania it had been cultivated since 1940s in Kagera region but decline in coffee prices in the world market in the 1990s resulted into more cultivation of the vanilla crop as an alternate crop in Kagera and Kilimanjaro regions. Vanilla which had a remarkable high price compared to coffee was consequently spread and grown in Tanga, Morogoro regions and Zanzibar Island. A study was undertaken to identify cultivars and examine the extent of genetic diversity of Vanilla planifolia using molecular technique. A total of 126 samples were randomly taken from Bulinda, Bakabuye and Kibona villages in Kagera Region, Mkunazini and Donge village in Zanzibar Island and Mudio and Kidia villages in Kilimanjaro Region. The deoxyribonucleic acid (DNA) extraction method that was used in this research was the Dellaporta protocol. DNA quantification was done by comparing band intensity of different concentrations of standard genomic DNA markers using agarose gel electrophoresis. For the optimization of PCR, three different components; dNTPs, Taq DNA polymerase and MgCl2 were tested in different combinations.Ten primers were selected for the Random Amplified Polymorphic DNA (RAPD) reactions. The results revealed genetic distances of 0.667, 0.705 and 0.805 for Kagera, Kilimanjaro and Zanzibar respectively for intra population diversity and 1.28 for interpopulation diversity. This indicates a narrow genetic diversity. Similarly altogether the 126 cultivars included in this study generated 53 bands of which only 27 were polymorphic this indicates a low level polymorphism. The fact that the vanilla cultivars from Kilimanjaro and Kagera did not markedly diverge genetically from the vanilla cultivars in Zanzibar island suggests a narrow genetic diversity of populations and probably present cultivars have been derived from common source parents and maintained over several decades. Exchange of cultivars between plantations and seedling selection may also have played a role.SUA -PANTIL