Corn stover (CS) or apple pulp (AP) were used to improve the anaerobic digestion performance of chicken manure (CM) or pig manure (PM), with the aim of adjusting carbon/nitrogen ratio and increasing the system stability compared to animal manures alone. This study was conducted in batch and semi continuously fed digester at laboratory scale. The results of batch tests showed that the optimal mixture ratios for CM/CS, CM/AP, PM/CS and PM/AP were 4:1, 2:1, 4:1, 4:1, respectively. In the semi continuous mode, inhibition to methane generation occurred when organic loading rate (OLR) of manures mono-digestion was higher than 2.4 g VS L(-1)d(-1). However, the co-digestion of chicken manure with apple pulp at ratio 2 allowed operation at OLR of 4.8 g VS L(-1)d(-1) and obtained the highest specific methane production (0.34 L g(-1) VSadded), due to its enhanced buffer capacity and nutrient balance. Fluorescence in situ hybridization revealed that the microbial community in digester fed with CM/AP mix was dominated by Methanosarcina and the remaining microorganisms mainly belonged to Methanobacteriales, both of which reflected the tolerance of inhibitors in this system. However, in digesters with other mixture (CM/CS, PM/CS, PM/AP), the negative impact of high levels ammonia and volatile fatty acids on sensitive Methanogenic Archaea resulted in serious decrease in the dominant species and finally caused the failure of anaerobic digestion. (C) 2017 Elsevier Ltd. All rights reserved.