The study was conducted to identify fungal pathogens associated with Cowpea (Vigna unguiculata [L.] Walp) seeds obtained from the South Western States of Nigeria. Three hundred seed samples of cowpea were collected from twenty (20) local governments across five States in the South West of Nigeria. The seeds were surface sterilized using 10% sodium hypochlorite, plated on Potato Dextrose Agar (PDA), and incubated at 25°C. The colonial, morphological, and molecular characteristics were used for the identification of the pathogens. For molecular identification, ITS Universal Fungi primer was used for the PCR analysis to amplify the extracted DNA. The results showed that A. niger, A. flavus, and B. theobromae were the most common with values of 7.77, 7.6,1, and 6.59% respectively. Ondo State had the highest level of disease incidence of 76.61%. This call for an integrated approach toward mitigating seed-borne fungi during post-harvest storage.