This work reports the occurrence of the fungal flora and evaluates the mycotoxigenic potential of Aspergillus genera in 63 samples of oil seeds and nuts (almonds, pistachio and sesame seeds). Fungal isolation and identification revealed the presence of 5 genera (Aspergillus, Penicillium, Cladosporium, Mucor and yeasts) with the predominance of Aspergillus section Nigri. A number of 138 strains of Aspergillus section Nigri and 91 of Aspergillus section Flavi were isolated and tested for their ability to produce ochratoxin A (OTA) and Aflatoxin, respectively. The detection of Aflatoxins and OTA production was carried out using thin-layer chromatography (TLC). Our results showed that 93.93% of Aspergillus carbonarius were able to produce OTA, but none of the Aspergillus niger aggregate was found to be an OTA-producer. Among the 91 Aspergillus section Flavi isolates, 88 were identified as Aspergillus flavus and 3 as Aspergillus parasiticus. All A. parasiticus were strong AFB and AFG producers. A percentage of 30.3% of A. flavus isolates produced AFB1, with levels ranging from 0.69 to 44.28 μg.g−1. The frequency of aflatoxigenic A. flavus strains was higher in pistachios (46.3%) than in almonds (30.3%) or sesame seeds (23.52%). Cyclopiazonic acid (CPA) and sclerotia production were carried out on CYA medium. All aflatoxigenic A. flavus strains produced CPA, whereas 29.2% produced sclerotia (L-type).