Fruit rot is the principal phytopathological problem of pipiana pumpkin (Cucurbita argyrosperma Huber) in the state of Guerrero. The aims of this research were to 1) identify the causal agent of southern blight on pumpkin fruits by morphological, pathogenic, and molecular analysis (ITS1, 5.8S, ITS2); 2) evaluate in vitro Trichoderma spp. strains and chemical fungicides; and 3) evaluate under rainfed field conditions, the strains that obtained the best results in vitro, combined with fungicides during two crop cycles. Number of commercial and non-commercial fruits at harvest, and seed yield (kg ha−1) were registered. Morphological, pathogenic and molecular characterization identified Sclerotium rolfsii as the causal agent of rot in pipiana pumpkin fruits. Now, in vitro conditions, the highest inhibition of S. rolfsii were obtained by Trichoderma virens strain G-41 (70.72%), T. asperellum strain CSAEGro-1 (69%), and the fungicides metalaxyl (100%), pyraclostrobin (100%), quintozene (100%), cyprodinil + fludioxonil (100%), and prochloraz (100%). Thiophanate-methyl only delayed growth (4.17%). In field conditions, during the spring-summer 2015 cycle, T. asperellum strain CSAEGro-1 + metalaxyl, and T. asperellum + cyprodinil + fludioxonil, favored the highest number of fruits and seed yield in the crop.