Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of cocoa pulp is crucial for developing chocolate flavor precursors. This fermentation is led by a succession of complex microbial communities where yeasts play key roles during the first stages of the process. In this study, we identified and analyzed the growth dynamics of yeasts involved in cocoa bean fermentation of six major cocoaproducing regions in Ivory Coast. A total of 743 yeasts were isolated, and were identified by sequencing of D1/D2 regions of 26S rDNA gene. These isolates included 11 species with a predominance of Pichia kudriavzevii (44,81 %), Pichia kluyveri (20,99 %) and Saccharomyces cerevisiae (18,97 %) respectively. In addition, the length polymorphism of the genetic marker ITS1-5.8S-ITS2 and PCR-RFLP analysis revealed an intraspecific diversity within the three-main species involved in cocoa fermentation of six major local regions in Ivory Coast. This intraspecific diversity could be exploited for selecting appropriate starter cultures.