A process for anaerobic digestion of cotton willow dust, pressmud and baggase after a preliminary alkaline aerobic digestion had been developed. The microbial ecologies during the aerobic digestion and anaerobic fermentation of these substrates were investigated, with respect to the isolation, identification and characterization of aerobic microorganisms. The study produced information on the survival of aerobic and facultative bacteria, actinomycetes and fungi, under anaerobic conditions.