Species within Aspergillus section Nigri and section Circundati are important sources of ochratoxin A (OTA) contamination in several foods and beverages such as cereals, grapes, spices, peanut, cocoa, wine, beer, and coffee worldwide. Few surveys showed the epidemiology, ecology, and distribution of black aspergilli occurring in crops from different Latin American regions. Within section Nigri, Aspergillus niger aggregate species are commonly the most prevalent, followed by A. carbonarius and Aspergillus uniseriate. Aspergillus ochraceus is the most important ochratoxigenic species included in the section Circundati. These species differ in their OTA-producing ability, since the percentage OTA-producer strains and the levels produced are variable. The OTA levels detected in grains and fruits also were variable, and it was shown that their damage affected the incidence of ochratoxigenic species and OTA contamination. Temperature and water activity were also key factors determining the Aspergillus section Nigri colonization and OTA accumulation in different commodities. The knowledge of the factors affecting preharvest and post-harvest contamination of foods by black aspergilla and OTA production is essential to improve the quality and safety of foods. Different strategies can be used to reduce the impact of Aspergillus and OTA accumulation. Alternative strategies to the chemical control can be biocontrol or the use of natural substances such as antioxidants and essential oils. The data presented in this review provide relevant information for using appropriate management strategies to reduce or prevent the development of ochratoxigenic species and OTA accumulation on different commodities relevant for Latin America.