The objective of this study was to determine the effect of natural co-culture of anaerobic fungi and methanogens on the methane production and lignocellulosic degradation of waste from rice, corn and sugarcane. Hu sheep rumen digesta was used to develop a natural co-culture of anaerobic fungus and methanogen. The substrates used in this study were rice straw (RS), rich husk (RH), corn stover (CS), corn cobs (CC), and sugarcane baggage (SB). Production of total gas and methane, utilization rates of reducing sugar, glucose, and xylose, lignocellulosic degradation and the activity of CMCase and xylanase were highest (P < 0.05) in CC, subsequently followed by RS, CS, SB, and RH. The pH was the lowest (P < 0.05) in RH, followed by SB, CS, RS, and CC. The highest formate concentration (P < 0.05) was found in RH, the subsequently followed by SB, CC, CS, and RS. Acetate concentrations were highest (P < 0.05) in CC, then in RS, CS, SB, and RH. Lactate was lowest in CC (P < 0.05), then in RS, CS, RH, and SB. Ethanol was also lowest (P < 0.05) in CC, following RS, CS, SB, and RH. Therefore, the CC and RS have the highest potential, the CS has a moderate potential, and the SB and RH have the lowest potential for methane production and lignocellulosic degradation by natural co-culture of anaerobic fungus and methanogen.