Two new ecological niche clustering approaches are presented in this paper: first, an importance/dominance evaluation model, based on both density and biomass, is devised to evaluate the importance (contribution) of a specific species in its community; second, an integrated index encoding approach is constructed to spatially cluster all dominant species at a sampling site. Two approaches are employed to study ecological niche clustering of the Huai River Basin zoobenthos in order to identify key regions for ecosystem restoration. Results show that habitat changes will significantly impact Corbicula fluminea (Müller), whereas influences on Corbicula nitens (Philippi) will be the least significant. Total phosphorus has the greatest impact on zoobenthos, and high-concentrated ammonia nitrogen is also detrimental. Decreasing the discharge of both phosphorus and ammonia nitrogen in the Huai River Basin is therefore required to facilitate restoration. Changing habitat parameters has only a limited effect on alteration of zoobenthos structure. The application of these niche clustering approaches has identified priority locations for ecological restoration in the Huai River Basin. Copyright © 2012 John Wiley & Sons, Ltd.