Aims To investigate the genotypic diversity and enzymatic activity of yeast flora isolated from spontaneous fermenting saps of various palm trees (Borassus aethiopum, Raphia hookeri, Elaeis guineensis) tapped for palm wines. Methods and Results PCR-restriction fragment length polymorphism of ITS-5.8S rDNA combined to 26S rRNA gene and/or the partial ACT1 gene sequencing were applied for yeast characterization, and their enzymatic profiles assessed by using API ZYM kits. Thirteen genera and 23 species were identified, with the highest diversity (14 species) in raffia wine. Saccharomyces cerevisiae was dominant and common to all palm wines. Some potentially pathogenic yeasts were also isolated. The majority of tested strains displayed high amylo-peptidase, phosphatase, beta-glucosidase and alpha-glucosidase activities and esterase activity. Conclusions Diverse yeast species colonized palm wines, among which some were related to a specific type of wine and the majority of them have the ability to digest starch, sugar, protein or lipid. Significance and Impact of the Study This study is a first step in understanding the significance of indigenous yeast flora of palm wines from Cote d'Ivoire. This knowledge is important as a tool for establishing new indigenous yeast collection; which could be used for the product quality improvement and as enzyme sources for biotechnological purposes.