Abstract: Index of biological integrity (IBI) is one of the most important and popular tools in assessing aquatic ecosystem health. This paper reviewed the selection of indicator species for IBI, its construction process, and its applications in assessing aquatic ecosystem health, summarized the commonly used candidate biological parameter indices of fishindex of biological integrity (F_IBI), benthosindex of biological integrity (B_IBI), and periphytonindex of biological integrity (P_IBI), and pointed out the feasibility and necessity of using microbe-index of biological integrity (M_IBI) to assess the health of aquatic ecosystem.