Aspergillus niger is abundant in most tropical soils and invariably, on the surface of yam tubers while still attached to the plant and on the root hairs during harvesting or storage. Naturally, the peridermic surface of the tubers function to exclude pathogen but damage caused by accidental incision or cut surface during weeding, insect attack and harvesting provide avenue for the infection. Aspergillus niger isolated from diseased yam in three zones in Nigeria synthesized cellulase which caused soft rot of the yam within nine days of inoculation. Microscopic and molecular analyses revealed two isolates of A. niger, P 1 and P 2, from different environment produced cellulase enzymes in significantly different proportions. When protein extracts from the infection were subjected to molecular exclusion chromatography, three peaks of absorption (A, B and C) were produced with only the components of peak A showing cellulase activity. Further fractionation of the components of peak A produced two absorption peaks (Aa and Ab) with only component Aa showing Cellulase activity. A. niger isolates, P 1 and P 2 showed considerable differences in the intensity of cellulase production suggesting that multiple strains of A. niger in the soil of yam-growing environments synthesized cellulase as transcriptional products in different manner underscoring the effect of physico-chemical properties of the soil on infectivity and virulence of the organism during yam rot.