Anaerobic sequencing batch reactor (SBR) was started-up by inoculating the nitrifying activated sludge. After an operation of 72 d, the bioreactor reached at steady state with ammonia and nitrite removal percentages higher than 95%. During operation, the sludge granulated in the reactor. The morphology and internal structure of sludge granules changed conspicuously, the density increased while the color changed from khaki to red. The average granular diameter grew from 1.2 to 3.69 mm, and its settling velocity accelerated from 107.68 to 118.49 m/h. Sludge granulation improved the tolerance to hydraulic shock loading, and reduced sludge washout (TSS < 0.028 g/L). The dominant bacterial communities (filamentous and cocci) in nitrifying activated sludge were replaced by irregular shaped ANAMMOX bacterial species gradually. An increase of ANAMMOX rate was achieved with the increasing granular diameter. SBR is a useful reactor to cultivate ANAMMOX granular sludge, while granular ANAMMOX sludge thus developed can be used as seeding sludge in a pilot-scale or full scale wastewater treatment plant.