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A Planktonic Integrity Index (PII) for the China’s largest alpine barrier lake (Jingpo Lake) was developed to assess the water quality of Jingpo Lake by using phytoplankton and zooplankton metrics. Phytoplankton and zooplankton assemblages were sampled at 26 sites in Jingpo Lake. A total of 140 species of phytoplankton and 92 species of zooplankton were obtained in the investigations. We used a stepwise process to evaluate properties of candidate metrics and selected five for the PII: Algal cell abundance, Species richness of algae, Trophic diatom index, Zooplankton Shannon index, and Zooplankton Margalef index. Evaluation of the PII showed that it discriminated well between reference and impaired sites and the discriminatory biocriteria of the PII were suitable for the assessment of the water quality of Jingpo Lake. The further scoring results from the 26 sites showed that the water quality of Jingpo Lake was fair to good. The results of analyses between PII and major environmental factors indicated that water temperature (WT), transparency (SD), dissolved oxygen (DO), potassium permanganate (CODMn) and total nitrogen (TN) were the main factors influencing on the composition and distribution of phytoplankton and zooplankton. Additionally, more metrics belonging to habitat, hydrology, physics and chemistry should be considered for the PII, so as to establish comprehensive assessment system which can reflect the community structure of aquatic organisms, physical and chemical characteristics of water environment, human activities, etc.