Marine zooplankton are key players in pelagic food webs, central links in ecosystem function, useful indicators of water masses, and rapid responders to environmental variation and climate change. Characterization of biodiversity of the marine zooplankton assemblage is complicated by many factors, including systematic complexity of the assemblage, with numerous rare and cryptic species, and high local-to-global ratios of species diversity. The papers in this themed article set document

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... advances in molecular protocols and procedures, integration with morphological taxonomic identifications, and quantitative analyses (abundance and biomass). The studies highlight several overarching conclusions and recommendations. A primary issue is the continuing need for morphological taxonomic experts, who can identify species and provide voucher specimens for reference sequence databases, which are essential for biodiversity analyses based on molecular approaches. The power of metabarcoding using multi-gene markers, including both DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid)templates, is demonstrated. An essential goal is the accurate identification of species across all taxonomic groups of marine zooplankton, with particular concern for detection of rare, cryptic, and invasive species. Applications of molecular approaches include analysis of trophic relationships by metabarcoding of gut contents, as well as investigation of the underlying ecological and evolutionary forces driving zooplankton diversity and structure.