A new stability evaluating system for ANAMMOX comprising three instability indices i.e. coefficient of variation ratio, coefficient of range ratio and coefficient of regression function derivative was established. Three lab-scale ANAMMOX reactors viz upflow anaerobic sludge blanket (UASB) reactor, upflow stationary fixed film (USFF) reactor and anaerobic sequencing batch reactor (ASBR) were compared for their stability based on the established criterion against the hydraulic and substrate concentration shocks. The results showed that all ANAMMOX reactors under investigation were more tolerant to the hydraulic shock than substrate concentration shock. The UASB reactor was the most stable reactor configuration towards substrate concentration shock, followed by the USFF reactor and ASBR. However, the ASBR proved the most tolerant to hydraulic shock, followed by the UASB reactor and USFF reactor. In terms of stability, UASB reactor was more suitable configuration compared with USFF reactor. The instability indices proved to be effective and explicit for the evaluation of ANAMMOX systems.