Gene diversity and population structure were analyzed in 14 natural teak ( Tectona grandisL.f.) populations in India belonging to Kerala, Madhya Pradesh, Gujarat and Orissa using microsatellite markers. The data collected through microsatellite marker studies from 550 trees of the natural teak populations in different geographic areas indicate that it has different genetic structure forming separate genetic clusters. Populations from Madhya Pradesh and Gujarat form the first cluster while Orissa is in the second cluster and Kerala populations except Nilambur fall in the third cluster. Phenotypically Nilambur teak stands are quite distinct among Kerala populations were reported earlier but this is the first report proving the uniqueness of Nilambur teak through DNA analysis. The results of this study using molecular markers also support and confirm that gene diversity within teak populations of teak are in higher percentage than the gene diversity among populations.