Argentina is among the top 20 legume producers in terms of tonnage. Cowpea (Vigna unguiculata [L.] Walp., cv. Cuarentón) contains a high concentration of protein, minerals, vitamins, and carbohydrates and a low lipid content, making it of great importance in human nutrition. The seeds of various legumes have been reported to be an important source of primary inoculum for various pathogenic fungi, including species of the genera Fusarium, Curvularia, Bipolaris, Alternaria, and Macrophomina, etc. Therefore, the objective of this study was to quantify the presence of fungi in cowpea seeds from two agricultural seasons and to identify the fungi present in different parts of the seedling (root, leaf, and petiole). The plant material was sown in Petri dishes with potato glucose agar with the addition of an antibiotic (streptomycin) to avoid bacterial contamination. For the seeds, 200 seeds of the Cuarentón variety were used. The results obtained were as follows: seeds from the 22/23 campaign: Trichoderma (11.5%), Fusarium (9%), Sordaria (4%), Alternaria (4%), Penicillium (3.5%), Aspergillus (2%), Bipolaris (0.5%), and Nigrospora (0.5%). Seed Campaign 23/24: Trichoderma (22%), Fusarium (7%), Curvularia (3%), Aspergillus (1.5%), and Nigrospora (0.5%). The fungi found in the sowing of the different parts of the seedling are the following: root: Fusarium and Exserohilum; leaves: Alternaria, Fusarium and Cladosporium; and petiole: Alternaria and Bipolaris. It is noteworthy that the genus Trichoderma is the fungus with the highest incidence levels in both campaigns. This microorganism stands out for being an excellent antagonist of fungal pathogens. Its use in the biological control of diseases is an indispensable tool today in the integrated management of pests and diseases of different crops. This work makes a first contribution to the search for native fungal antagonists in cowpea crops, in order to improve the control of fungal diseases.