The most significant food crops in West Africa are edible yam types (Dioscorea spp.). Farmers have been extremely worried about yam rot brought on by a fungal infection. The objective of the study was to discover environmentally friendly Trichoderma species from yam tubers using a phylogenic technique and to assess their biocontrol capabilities. Thirty samples of both healthy and diseased yam tubers were taken aseptically from farms in the Osisioma Ngwa Local Government Area of Abia State, Nigeria, and sent to the laboratory for microbiological investigation. The samples were analyzed using conventional microbiological techniques, and dual culture assay method was also used to test antagonistic response. Fusarium sp., Aspergillus niger, and Penicillium sp. were the fungi isolated and identified as pathogens, while Trichoderma strains, Trichoderma asperellum (JN004180.1), and Trichorderma koningiopsis (MF5087061) were identified as the isolated biological control agent. A. Niger’s growth was inhibited by the biological antagonist T. asperelleum by 78.6%, Penicillium sp. by 51.2%, and Fusarium sp. by 69.2%, whereas A. Niger’s growth was inhibited by the antagonist fungus T. koningiopsis by 76.6%, Penicillium by 46.1%, and Fusarium by 61.5%. This study demonstrated the ability of two strains of the fungus Trichoderma, Trichoderma asperellum (JN004180.1) and Trichorderma koningiopsis (MF5087061), to biocontrol the common pathogenic fungi that destroy yam in South-Eastern Nigeria and other parts of the world. It is crucial that Nigeria and sub-Saharan Africa commercialize the Trichoderma sp. biological control agent since doing so will make it easily accessible to low-income farmers.