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Aquatic invertebrate diversity reflects water quality and the health of aquatic ecosystems and should be monitored as an essential feature of freshwater ecosystems. The resting eggs of aquatic invertebrates in sediments populate the overlying water. The diversity of invertebrates in waters and their resting eggs in sediments in Baiyangdian Lake, Xiongan, North China, were assessed using high-throughput sequencing (HTS) with a pair of 18S rRNA gene adaptor-linked primers. The total of 99 operational taxonomic units (OTUs) derived from 353,755 invertebrate sequences (mostly zooplankton) were revealed by this study. A total of 50 species in the water samples including 20 rotifers, 11 copepods, 1 cladoceran and 18 other species were sorted out. In the sediment 37 species, including 21 rotifers, 3 copepods, 1 cladoceran and 12 other species, were identified. There were 24 species in common between water …