The effect of different concentrations of ammonia (1.0-7.0 g/L) during mesophilic anaerobic digestion with fiber or liquid digestate as inoculum was examined. Evolution of microbial community within fiber and liquid digestates was quantitatively assessed by the intact lipid analysis methods and qualitatively by DNA fingerprint methods in order to determine their resistance to ammonia inhibition. The results showed that an increased level of total ammonia nitrogen prolonged the lag phase of fiber digestates while reduced the metabolic rate of liquid digestates. Fiber digestates had 19.6-50.9-fold higher concentrations of phospholipid fatty acids (PLFA) compared to liquid digestates, whereas concentrations of phospholipid ether lipids (PLEL) in the fiber digestates were only 2.91-17.6-fold higher compared to liquid digestates. Although the cell concentration in liquid fraction was far lower than that in the fiber one, the ammonia-resistant ability and the methanization efficiency of the liquid digestate was superior to the fiber digestate. The bacterial profiles were affected more by the type of digestate inoculum compared to the concentration of ammonia. Principal component analysis indicated that the lipids technique was superior to the DNA technique for bacterial quantification but detected less archaeal diversity.