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Benthic macroinvertebrates play important roles in shallow lake ecosystems. Several studies based on qualitative comparisons of the amount of macrophytes were carried out to relate benthic macroinvertebrate assemblages to habitat conditions in shallow lakes. Our main aim was to analyze the effects of habitat type and trophic state on taxonomic composition and abundance of benthic macroinvertebrates in lowland shallow lakes based on quantitative classification of habitat types. The benthic macroinvertebrate assemblages were investigated in eight shallow lakes of eastern China in four seasons. A total of 33 species was collected from these lakes, including four Oligochaeta, eight Chironomidae, eight Gastropoda, four Bivalvia and nine other miscellaneous species. According to the ratio of the dry weight of macrophytes to the dry weight of phytoplankton, the study lakes were separated into three lake types; macrophyte-dominated, transitional, and algae-dominated regions. The total abundance of macroinvertebrates was significantly higher in the group of algae-dominated regions than in the macrophyte-dominated regions. Scrapers had the highest abundance in the macrophyte-dominated regions. Univariate and multivariate analyses results showed that abundance, biomass and characteristic species of benthic macroinvertebrates were affected by their habitat types. The abundance and biomass of macroinvertebrates showed significant positive correlations with the trophic state index (TSI). TSI and turbidity were significantly correlated with DC1 (Axis 1 of detrended correspondence analysis), while Chlorophyll a and the ratio of the dry weight of macrophytes to the dry weight of phytoplankton were significantly correlated with DC2. The findings indicated that the habitat type and trophic state were the key factors determining the structure of macroinvertebrate assemblages in lowland shallow lakes. Our study was one of the few studies that had demonstrated the distinct influence of habitat type on macroinvertebrate assemblages in shallow lakes according to the ratio of the dry weight of macrophytes to the dry weight of phytoplankton.