Abstract: The effect of anaerobic digestion on the microbial flora and modeling of process parameters in the digestion of some animal dung like cow (CD), swine (SD), rabbit (RD), poultry (PD) and goat dung (GD) were verified. The digestion study was batch operated within a 98 days retention period using 50 L capacity metallic prototype digester. Average daily volume of gas production for each of the systems was 44, 40, 37, 33 and 31 dm3/total mass of slurry (TMS), respectively. Microbial analyses of the different dung before the digestion indicated the presence of microbes such as Proteus sp. Salmonella typhosa, Aerobacter cloacae, E. coli, B. subtilis, while isolation and identification of the microbes at the end of digestion showed that some of the initial microbes died during digestion giving way to other species of microbes like Clostridium perfringes and Salmonella typhimorium. Mathematical modells derived using computer aided regression analysis also indicated that biogas production of animal wastes can be predicted based on digestion time and total microbial viable count (TVC). Overall results indicate that anaerobic digestion does not completely destroy the pathogens found in animal wastes but reduces them to a safe level for handling and use. The results further show that cow, swine and rabbit dung are better starters or blending wastes for the low-yielding ones.