The presence of fungi of the genus Aspergillus must be investigated because it is related to the diminishment of quality and consequently to the risk to health of consumers due to the possible production of mycotoxins. In this context, this study was performed with the aim to evaluate the presence of Aspergillus species in cocoa beans produced in the state of Rondônia, Brazil, as well as verify the toxigenic potential of these species and the effect of the geographical origin on the incidence of toxigenic and non-toxigenic species of fungi. The technique of logistic regression was used to estimate the probability of occurrence of the genus Aspergillus. A total of 185 Aspergillus were identified. Among the tested Aspergillus carbonarius, 79.41% produced ochratoxin on levels from 0.08 to 44.09 µg/g in the culture medium. For the other Aspergillus species, the production potential was only assessed, and 3.13% of the A. niger presented potential to produce OTA and 83.33% of A. flavus which was able to produce aflatoxins. The presence of these toxigenic species indicates a potential risk of mycotoxin in cocoa beans and in their derived products in the studied region. Besides, the occurrence of Aspergillus species differed in function of geographical coordinates and temperature, presenting higher probability of occurrence on cocoa beans of municipalities located in Southern Rondônia, Brazil.