Aims: 104 samples were collected from the west region and the coastal plain of Cameroon during two coffee campaigns, 2009 and 2010. Two coffee processes were evaluated (wet and dry processes) at different stages from harvesting to storage. Study Design: Food contaminants. Place and Duration of Study: Food Microbiology Laboratory, Department of Food Science and Nutrition (ENSAI) University of Ngaoundere; UMR 95 Qualisud, CIRAD of Montpellier, between May 2009 and September 2012. Methodology: Fungi profile was evaluated by direct plating techniques and identified using morphological and molecular tools. OTA levels were analyzed using HPLC technique after extraction and filtration using an immunoaffinity column. Results: Results obtained revealed an overall percentage of fungal contamination between 60-92% in 2009 and 70-90% in 2010. There was no ecological difference in the composition of ochratoxigenic species present in five sites. Coffee beans sampled in 2009 had a colonization incidence of 18-40% A. carbonarius, 12-22% A. niger, 3-15% A. ochraceus while those of 2010 had a colonization incidence of 15-30% A. carbonarius, 35-40% A. niger, and 2-7% A. ochraceus. Fungal diversity was not correlated with the geographical origin, coffee cultivar and processing method. There was no difference between the processes studied in terms of occurrence of ochratoxigenic fungi. OTA levels were mostly below the recommended standards although some isolated cases of extreme contamination were observed in 2009. A higher level of OTA was detected in the presence of A. niger, A. carbonarius and A. ochraceus than when only A. niger was present. Conclusion: The important fungi with the potential to produce OTA in Cameroonian coffee beans are A. carbonarius and A. niger. These two species were predominant on each type of coffee beans. It was also observed that once a toxigenic strain was isolated from a coffee sample, the sample contained OTA.