SRP176431 PRJNA513188 Time-series V9 metabarcoding analysis of zooplankton diversity of the NW Atlantic continental shelf The 18S rRNA V9 hypervariable region was sequenced for 26 zooplankton samples collected from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring Surveys by the US Northeast Fisheries Science Center during 2002-2012. A total of 7,648,033 sequences and 22,072 operational taxonomic units (OTUs) were identified and classified into 28 taxonomic groups of plankton. Comparative analysis of molecular (V9 sequence numbers) and morphological (abundance counts) focused on 7 taxonomic groups of holozooplankton and revealed similar patterns of variation among years and regions. This study demonstrates the potential of metabarcoding for time-series analysis of zooplankton biodiversity, ocean ecosystem assessment, and fisheries management.