Inocula play an important role in anaerobic reactor startup by balancing the populations of Syntrophobacter and methanogens. Such balances make syntrophic metabolism thermodynamically feasible in anaerobic digestion. In this study, the effect of inocula on the performance of dairy manure digestion was investigated by analyzing the change in volatile fatty acids (VFA), total solids (TS), volatile solids (VS), specific biogas production (SGPR), and specific methane production (SPMP) as well as scanning and transmission electron micrographs. The study was performed at four treatments. Treatment one was granular sludge (GM); treatment two was non-granular sludge (SM); treatment three was mixed culture from an anaerobic lagoon (LM); while the fourth treatment (the control denoted MM) did not receive any exogenous inocula. In addition, stirred and unstirred conditions were maintained in the reactors to determine their effect on reactor startup. Performance ranking based on the SGPR and SPMP of treatments (in descending order) was: GM, SM, LM and MM under stirred conditions. Under unstirred conditions, performance ranking (also in descending order) was: SM, GM, LM, and MM. Results of the examination of microcolonies in the granular, non-granular sludge, and dairy manure suggest that syntrophic juxtaposition of methanogens and Syntrophobacter in granular inoculum was common while it was less visible in non-granular sludge, and completely absent in dairy manure. Published by Elsevier Ltd.