The changes in microbial morphologies and structures of aerobic granules under different organic loading rates (OLR) and their tolerance toward free ammonia (FA) and free nitrous acid (FNA) were studied in this research. The development of aerobic granules was carried out in 3 stages using sequencing batch reactor, (i) synthetic wastewater with OLR of 1.2 kg/m3 day, (ii) low strength real domestic wastewater with OLR of 0.13 kg/m3 day, and (iii) domestic wastewater with added external carbon source to give an OLR of 0.6 kg/m3 day. It was found that OLR as low as 0.6 kg/m3 day was able to develop and maintain the integrity of aerobic granules. After a starvation period, aerobic granules were capable to immediately responded to the increase in substrate. Microscopic images showed that different microbial morphologies and structures were found in aerobic granules at the three different stages. The inhibitory studies of FA and FNA on the activity of aerobic granules reveals that FA at a concentration up to 36.9 mg NH3-N/L did not inhibit the oxygen uptake rate (OUR) of aerobic granules. However, FNA started to inhibit the OUR at 0.015 mg HNO2-N/L and completely stopped the oxygen consumption at around 0.134 mg/L HNO2-N/L.