Functional bacterial consortiums that effectively tolerate high organic loading rates (OLR) were isolated using an organic shock-loading-to-extinction approach. The aerobic sludge granules were cultivated at low OLR and microbial community was challenged with stepwise increase in organic loadings to isolate functional consortiums. Strain Zoogloea resiniphila and at least two uncultured strains, Acinetobacter sp. clone JT2 and bacterium clone P1D1-516, formed the functional consortium of the aerobic granules present under a high OLR. The loss of these uncultured strains caused protein leakage from granules, thereby destabilizing the granules. The proposed organic shock-loading-to-extinction approach is effective in isolating the functional consortium from aerobic granules under high OLR.