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Aerobic granular sludge (AGS) is usually considered to be a biofilm system consisting of granules only, although practical experience suggests that flocs and granules of various sizes co-exist. This study thus focused on understanding the contribution of flocs and granules of various sizes to nitrification in a full-scale AGS-based wastewater treatment plant (WWTP) operated as a sequencing batch reactor (SBR). The size distribution in terms of total suspended solids (TSS) and the distribution of the nitrifying communities and activities were monitored over 14 months. Our results indicate that AGS is a hybrid system in which flocs (<0.25 mm) play a critical role in nitrification. AGS consisted of 36 % flocs and 50 % large granules (>2 mm) at a TSS concentration of 4.7 ± 0.7 gTSS L<sup>-1</sup>. The growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in large granules was limited due to the high mass transfer limitation in biofilm and the high solids retention time (SRT) of flocs, where favorable conditions for the growth of nitrifiers were maintained during the warm season. The specific activities of the small aggregates (<1 mm) were 5 to 15 times higher than those of large granules. As a result, flocs contributed >50 % to nitrification during the warm season, whereas granules >1 mm contributed <20 %. Such predominance of flocs in nitrification became problematic in the cold season when the minimum SRT of NOB increased to values similar to the floc SRT, resulting in 79 % loss of the NOB. Consequently, NOB activities dropped, and elevated effluent nitrite concentrations of several mgN L<sup>-1</sup> were monitored. We suggest operating AGS systems similarly to hybrid systems in order to promote the enrichment of NOB in the granules by controlling the floc SRT at low values smaller than the minimum SRT of NOB throughout the year.