Five yam tuber varieties were investigated for microorganisms that cause yam tuber rot from five local government areas of Benue State, Nigeria, between the months of March 2014 to March 2015. Five fungi species: Aspergillus niger, Rhizopus stolonifera, Botryodiplodia theobromae, Fusarium oxysporum, Penicillium marnessei and four bacteria species: Serratia marcescens, Erwinia carotovora, Klebsiella oxytoca and Pseudomonas aeruginosa were consistently isolated. Pathogenicity test carried out confirmed these organisms as the pathological agent of the rot. Antimicrobial activity of five plant aqueous extracts: Terminalia catapa (common name fruit), Passiflora edulis (passion fruit), Daniella oliveri (Chiha-Tiv), Ceiba pentandra (Vambe-Tiv), Jatropha tanjorensis (Catholic plant) was carried out on the isolated microorganims and they showed varing degrees of inhibition, the aqueous extract from Passiflora edulis, Ceiba pentandra and Jatropha tanjorensis were able to inhibit all the fungi completely.