Aerobic granules seeded with activated sludge flocs and pellets (obtained from activated sludge flocs) were cultivated in two sequencing batch reactors and their characteristics were compared. Compared with granules seeded with activated sludge flocs, those seeded with pellets had shorter start-up time, larger diameter, better chemical oxygen demand removal efficiency, and higher hydrophobicity, suspended solid concentration, and Mg2+ content. The different inocula led the granule surface with different microbial morphologies, but did not result in different distribution patterns of extracellular polymeric substances and cells. The anaerobic bacterium Anoxybacillus sp. was detected in the granules seeded with pellets. These results highlighted the advantage of pellet over activated sludge floc as the seed for aerobic granulation and wastewater treatment.