Rice is one of the most consumed cereals in Brazil and around the world. Due to the major health impact of rice consumption on populations, studies about its quality have great importance. The present study determined the mycobiota of soil, field, processing and market rice samples from two production systems in Brazil, dryland in the state of Maranhão and wetland in the state of Rio Grande do Sul. These areas are distinct agroclimatic zones. A total of 171 rice and 23 soil samples were analyzed. A high differentiation was observed in the composition of the fungal communities found in the two production systems, as the wetland presented greater fungal incidence and biodiversity. It was observed that toxigenic species from Aspergillus section Flavi and Fusarium, present in the field, may infect rice grains pre or postharvest and may persist into the final product.