The contamination of staple foods by mycotoxins is a significant issue in sub-Saharan Africa, particularly the presence of aflatoxins in raw peanuts and peanut-based products. This contamination has severe health and economic consequences. The main aflatoxin-producing fungi belong to Aspergillus section Flavi and are grouped in three main clades: A. flavus, A. tamarii and A. nomius, newly qualified as Flavi, Kitamyces and Nomiarum series respectively. The present study assessed the biodiversity of Aspergillus section Flavi species along the peanut paste production chain in the Korhogo region in northern Côte d'Ivoire. A polyphasic approach was used to identify 256 potentially aflatoxigenic strains isolated on AFPA medium. Experiments included (i) morphological characterization, (ii) aflatoxin production on PDA medium, (iii) molecular identification using a PCR-DGGE method and DNA sequencing, and (iv) phylogenetic analyses. Three species of A. flavus clade were isolated. The most prevalent was A. flavus, which comprised mainly aflatoxin-producing strains but also atoxigenic strains, followed by A. aflatoxiformans and A. korhogoensis. The latter two produced B and G aflatoxins at higher levels than A. flavus, which only produced B aflatoxins. A. aflatoxiformans, A. korhogoensis and aflatoxigenic A. flavus strains were mainly isolated after the stages of peanut pod drying and storage in villages, as well as after seed storage by wholesalers and retailers. However, AF production requires confirmation on most appropriate inducing media. The study also indicates that the PCR-DGGE method when combined with a multi-locus phylogenetic analysis is an effective strategy for discriminating and identifying Aspergillus section Flavi species, particularly those in the A. flavus clade.