Saccharomyces cerevisiae has a major role in the natural fermentation of traditional alcoholic beverages. To produce special characteristics of palm wine, a complex community is involved in the natural fermentation process and other yeast species could also contribute metabolically. In this study, we studied a non-Saccharomyces group of yeast isolated from natural fermentation of palm wines from different areas of Indonesia. We collected the palm wine samples from five different regions: Central Sulawesi, Lombok Island, Maluku, West Java, and West Papua. All samples were cultured in media and three of those were investigated by culture-independent method to view a deeper profile of yeast community. Eighty-seven strains of yeasts were isolated and belonged to S. cerevisiae (63.2%) and 32 strains were non-Saccharomyces group identified to 10 species. This composition was emphasized by next generation sequencing revealing that 78.0-96.4% of total sequences were S. cerevisiae and only three amplicon sequence variants belonged to other species in the Saccharomyces group, while 79 ASVs were grouped to non-Saccharomyces. These results reflect the diversity of non-Saccharomyces during the natural fermentation of palm wine which might have an essential role on constructing flavour characteristics.