Six microorganisms: four fungi-Aspergillus niger, Aspergillus flavus, Rhizopus stolonifera, Penicillium marneffei, two bacteria-Erwinia carotovora and Pseudomonas aeruginosa were isolated and identified from three rotten Dioscorea alata (water yam) varieties from two sites each in two local government areas of Benue State, Nigeria, in West Africa, between the months of May 2014 and May 2015. Pathogenicity test carried out using the microorganisms confirmed them to be the pathological agents of the rot. Antimicrobial activity test with aqueous extracts of nine plants: Terminalia catapa, Passiflora edulis, Daniella oliveri, Ceiba pentandra, Jatropha tanjorensis, Azadirachta indica, Carica papaya, Moringa oleifera, and Mangifera indica of fresh and dry material showed that three pathogens, Rhizopus stolonifera (fungi), Erwinia carotovora and Pseudomonas aeruginosa (bacteria) isolated were completely inhibited each by a plant. The result obtained shows that Passiflora edulis had the best antimicrobial activity for both fungi and bacteria; indeed it inhibited completely Rhizopus stolonifera which was stubborn with most of the other plants. Azadirachta indica, Carica papaya, Moringa oleifera, and Mangifera indica were also able to inhibit most of the fungi but not completely. Terminalia catapa and Jatropha tanjorensis were most effective against the bacteria. Erwinia carotovora was completely inhibited by Terminalia catapa and Pseudomonas aeruginosa was completely inhibited by Jatropha tanjorensis. Daniella oliveri and Ceiba pentandra had the least inhibition against the isolates. Generally, the fresh plant extract shows more activity as compared to the dry plant extract.