Microbial succession refers to the changing microbial population in a natural of disturbed system. The aim of this study was to isolate and determine bacterial succession in anaerobic fermentation. Cow dung was collected from Oja-Oba in Ekiti State, Nigeria while the corn cob was collected from Ajayi Farms in Akure, Ondo State, Nigeria, and transported to Afe Babalola University (ABUAD) Farms, where it was ground into smaller pieces. One hundred kilograms of cow dung was mixed with water and transferred to digester A, 100 kg of corn cob was transferred to digester B and 50 kg each of cow dung and corn cob were transferred into digester C. Microorganisms were isolated using pour plate method from day 1 of the fermentation period and at 5 days intervals for the 30 days fermentation period. The bacterial isolates were identified on the basis of their morphological, biochemical characteristics and molecular analysis (DNA extraction, Polymerase Chain Reaction and gene sequencing). Some of the bacteria isolated were Escherichia coli CFT073, Arthrobacter citerus strain NEB577, Klebsiella aerogenes strain AR 0018, Pseudomonas aeruginosa PA01 and Acinetobacter lactucae strain ANC405. Microbial succession of bacteria also showed the dominant organisms belong to Phylum Proteobacteria, followed by phylum Firmicutes and phylum Acinetobacteria. The amount of gas compressed after fermentation in the digesters varied. Digester A- 60kg, Digester B- 12.5kg and Digester C- 64kg with percentage weight of gas of 54%, 50% and 56% respectively. The result from this experiment clearly showed that the anaerobic fermentation of cow dung and corn cob involved the interaction between diverse microbial populations at various stages of fermentation.