Bambara groundnut is the main food legume after cowpea, especially in rural areas in Burkina Faso. Due to inappropriate production and storage conditions, the seeds are susceptible to contamination by several fungi. Therefore, the present study was conducted to isolate and identify the postharvest fungi associated with Bambara groundnut seeds produced in Burkina Faso. To do this, a total of 99 seed samples were collected in the three agro ecological zones of Burkina Faso. The sanitary analysis of the seeds was carried out using the blotting paper method with slight modifications. The isolation and purification of the isolates was performed on Potato Dextrose Agar medium while their identification was done through macroscopic and microscopic phenotypical characterization using different culture media (Malt Extract Agar and Czapeck Dox Agar) and different identification keys. A total of 421 fungal strains were isolated and the predominant genera were Aspergillus belonging to section flavi (66.84%), nigri (59.04%), and Macrophomina (26.49%). This study shows that Bambara groundnut seeds produced in Burkina Faso are contaminated by several fungal strains and that seed infection rates by these fungi differ according to the agro-ecological zones. Post-harvest and storage techniques need to be improved to limit crop losses.