Tropical fruit wines are gaining importance for its health benefits. However, the potential is unexplored in India and this work of isolation of indigenous yeast strains from the tropical fruit was undertaken. 28 strains of yeasts were isolated from tropical fruits, Syzygium cumini (Linn.) Skeel (Jamun) and Garcinia indica (Choisy) (Kokum) on a selective medium. The screening parameters were glucose and ethanol tolerance. Three most glucose and ethanol tolerant cultures were selected by testing tolerance for glucose (10-25% w/v) and ethanol (6-15 % v/v). Further characterization of these 3 cultures was carried out using biochemical and molecular test by sequencing internal transcribed spacer (ITS) region. Infer molecular phylogeny established that the three isolates viz, FJ 10, JR 01 and KF 01 were Saccharomyces sp. FJ 10, Candida tropicalis JR 01, Saccharomyces sp. KF 01 respectively. Till date to the best of our knowledge we are the first to report the isolation of tolerant Saccharomyces species from Jamun and Kokum fruits. Further studies on fruit wine production from the selected isolates showed promising results.