Sixteen fonio millet and 17 sesame samples were analysed for incidence of moulds, especially aflatoxigenicAspergillusspecies, in order to determine the safety of both crops to consumers, and to correlate aflatoxin levels in the crops with levels produced by toxigenic isolates on laboratory medium. Diverse moulds includingAlternaria,Aspergillus,Cercospora,Fusarium,Mucor,Penicillium,RhizopusandTrichodermawere isolated.Aspergilluswas predominantly present in both crops (46–48%), and amongst the potentially aflatoxigenicAspergillusspecies,A. flavusrecorded the highest incidence (68% in fonio millet; 86% in sesame kernels). AllA. parvisclerotigenusisolates produced B and G aflatoxins in culture while B aflatoxins were produced by only 39% and 20% ofA. avusstrains isolated from the fonio millet and sesame kernels, respectively. Aflatoxin concentrations in fonio millet correlated inversely (r = −0.55;p = 0.02) with aflatoxin levels produced by toxigenic isolates on laboratory medium, but no correlation was observed in the case of the sesame samples. Both crops, especially sesame, may not be suitable substrates for aflatoxin biosynthesis. This is the first report onA. parvisclerotigenusin sesame.