Various yam species are cultivated but white yam (Dioscorea rotundata Poir.), water yam (Dioscorea alata L.) and yellow yam (Dioscorea cayenensis Lam.) are among the most cultivated in Nigeria. The Susceptibility of three tubers of Dioscorea species (D. rotundata, D. alata and D. cayenensis) to dry rot pathogens was investigated. Isolation was made from rotted tuber tissues, followed by pathogenicity test and identification of isolates; two fungal species Aspergillus niger and Rhizopus stolonifer were isolated and identified as the major fungi causing yam tuber dry rot in the study area. There was significant difference (P<0.05) in the susceptibility of the various Dioscorea tuber species studied to rot caused by Aspergillus niger [D. rotundata (20mm), D. alata (11mm) and D. cayenensis (3.5mm)] and  Rhizopus  stolonifer [ D. rotundata (17.5mm), D. alata (10mm) and D. cayenensis (2mm)]. The phytochemical contents of the three tubers of Dioscorea species examined also varied significantly, with the bioactive substances of D. cayenensis and D. alata relatively higher when compared to D. rotundata. Therefore, this research reveals that three metabolites; Saponin, Flavonoid and Tanin constitute the major trait for resistant ability of D. cayanesis and D. alata to dry rot causing pathogen.  Therefore, it is necessary that the differences in susceptibility be considered when developing yam barns. Also, researchers should work on genetically improving the susceptible white yam (D. rotundata) which is commonly eaten by millions of Nigerians with a possibility of increasing the quantities of the deficient phytochemicals.