Cocoa beans are the principal raw material of chocolate manufacture.The beans are subject to post-harvest treatments in the first stage in chocolate production. The current study is designed to investigate the incidence of mycoflora in cocoa beans samples collected from Yamoussoukro and Soubré (Côte d'Ivoire) and the presence of ochratoxinogenic fungi on these samples using direct and dilution techniques. In this work, we evaluated the correlation between physicochemical factors (moisture content and pH) and fungi and mycotoxins contamination. This study highlights the physicochemical composition of cocoa beans, fungal contamination frequency and the fungus population description in different samples of cocoa beans. Our results revealed that the fungi contamination frequency varies according to physicochemical factors; on the one hand it increases proportionally to the moisture content. On the other hand, it decreases with the increase of pH rate. Mycotoxicologically, these results revealed the importance of the initial rate of pollution with a ochratoxinogenic species, as it reflects the risk of the toxinic impregnation, in other words, the higher the rate is, the more considerable the risk of finding mycotoxins in foodstuffs is.