Abstract The mycoflora of blackgram ( Vigna mungo) and aflatoxin production was investigated during storage. At harvest, seeds carry a combination of field and storage fungi. Species of Alternaria, Cladosporium, Fusarium and Curvularia were predominant. These moulds gradually disappeared in storage, though Alternaria and Fusarium survived in storage for a comparatively long period. Seed infection by Aspergillus flavus and Penicillium citrinum was observed during harvesting. Their density increased considerably in storage along with A. terreus, A. niger, A. ochraceus, Rhizopus stolonifer and Chaetomium spp. Almost 70% of Aspergillus flavus isolates were found to be toxigenic. Aflatoxin contamination in storage depended on the storage system: closed metal bins restricted air exchange, so reducing the oxygen which caused lower production of aflatoxins. Greater amount of aflatoxins were detected in samples stored in gunny bags during the wet season.