Rice cultivation is one of the most important agro-economic activities in many countries, and the correct seed storage between production cycles is essential for crop success. In Guinea-Bissau, mangrove swamp rice (MSR) is a highly productive rice cropping system, thus providing surplus for sale. Depending on storage conditions, rice grains may present moisture, insects, or the development of fungi that might affect crop productivity. Considering different rice varieties and storage conditions, samples were collected from 30 farmers within 13 villages across the main MSR-producing regions. Stored rice was used to isolate and identify seed-borne fungi through DNA barcoding, to test aflatoxin content, and to evaluate seed germination rates. Polyethylene bags (the container), raised wooden platforms, and storage rooms (the structures) are the most used facilities. Hermetic containers were recorded mainly in Oio. A total fungal richness of 18 genera was found, and 16 different species were identified. The most represented fungal genera are Aspergillus, Curvularia, and Bipolaris. Despite the presence of aflatoxin-producing fungal samples, they did not present concerning levels for human consumption, and the germination rate was not affected regardless of storage structures. These results provide a baseline on fungi occurrence in stored MSR seeds from traditional facilities in Guinea-Bissau.