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[Display omitted] • The invertebrate OTU abundance (%) in wetland showed that Cnidaria > Porifera > Rotifera > Mollusca > Annelida > others. • 'Simpson' diversity index was the most effective to distinguish the differences in invertebrate communities. • The class-level alpha diversity showed higher recognition than other taxonomic levels. • Insecta, Ascidiacea, and Monogononta were biomarkers for lake, river, and estuary habitats, respectively. • Explanation of environmental factors on OTU richness showed the taxon-level tendency phylum > class > order > family > genus. Invertebrates play vital roles in maintaining biodiversity and food web structure. However, it is difficult to identify invertebrate taxa across complex habitats due to the limitation of traditional morphology. In subtropical wetlands, environmental DNA (eDNA) metabarcoding was used to characterize the composition and diversity of aquatic invertebrates and analyze the environmental impacts on invertebrate community structure. According to the relative abundance (%) of invertebrate OTU richness, 30 sampling sites in wetlands were clustered into six zones, which exhibited significant spatial (i.e., wetland type-specific) differences in taxonomic composition. The relative OTU abundance (%) at the phylum level showed that Cnidaria (48.5%) > Porifera (19.4%) > Rotifera (11.0%) > Mollusca (9.2%) > Annelida (5.3 ± 2.8%) > others (less than 2.2%). Of the five alpha diversity indexes, 'Simpson' was the most effective index to distinguish the spatial differences in invertebrate diversity, and the class-level alpha diversity showed higher recognition than other taxonomic levels. The class-level biomarkers that could indicate the habitat-specific composition of local invertebrates were Insecta, Cnidaria, Hydrozoa, and Gastropoda in the inflow river; Ascidiacea and Demospongiae in the fluvial wetland; Clitellata, Gymnolaemata, and Monogononta in the lacustrine wetland; and Echinoidea in the estuarine wetland. The associations between environmental factors and invertebrate OTU richness based on redundancy analysis showed the taxon-level tendency of phylum (78.5%) > class (73.4%) > order (69.3%) > family (64.9%) > genus (61.2%). Our results demonstrated that aquatic invertebrate diversity profiling by environmental DNA metabarcoding can effectively reflect the composition, diversity and biomarkers of invertebrate communities. In the future, because of its great application potential, the eDNA technique may play an important role in biomonitoring complex water environments. [ABSTRACT FROM AUTHOR]