Mycological investigation of various foods (mainly cowpea, groundnut, maize, rice, sorghum) and agricultural soils from two states in north-central Nigeria (Nasarawa and Niger), was conducted in order to understand the role of filamentous fungi in food contamination and public health. A total of 839 fungal isolates were recovered from 84% of the 250 food and all 30 soil samples. Preliminary identifications were made, based on macro- and micromorphological characters. Representative strains (n = 121) were studied in detail using morphology and DNA sequencing, involving genera/species-specific markers, while extrolite profiles using LC-MS/MS were obtained for a selection of strains. The representative strains grouped in seven genera (Aspergillus,Fusarium,Macrophomina,Meyerozyma,Neocosmospora,NeotestudinaandPhoma). Amongst the 21 species that were isolated during this study was one novel species belonging to theFusarium fujikuroispecies complex,F. madaensesp. nov., obtained from groundnut and sorghum in Nasarawa state. The examined strains produced diverse extrolites, including several uncommon compounds: averantinmethylether inA. aflatoxiformans; aspergillimide inA. flavus; heptelidic acid inA. austwickii; desoxypaxillin, kotanin A and paspalitrems (A and B) inA. aflatoxiformans,A. austwickiiandA. cerealis; aurasperon C, dimethylsulochrin, fellutanine A, methylorsellinic acid, nigragillin and pyrophen inA. brunneoviolaceus; cyclosporins (A, B, C and H) inA. niger; methylorsellinic acid, pyrophen and secalonic acid inA. piperis; aspulvinone E, fonsecin, kojic acid, kotanin A, malformin C, pyranonigrin and pyrophen inA. vadensis; and all compounds inF. madaensesp. nov.,Meyerozyma,NeocosmosporaandNeotestudina. This study provides snapshot data for prediction of food contamination and fungal biodiversity exploitation.