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Abstract Taxonomic discussions often permeate the broader scientific community slowly, yet they may hold more relevance than typically assumed. In many zooplankton groups, identification issues arise from cryptic species complexes, increasingly revealed by molecular approaches, and from groups with high morphological similarity. These challenges can lead to substantial uncertainties in species-level identification, questioning whether the expected species are truly covered and whether those sharing names across ecosystems are indeed distinct entities. This review provides a condensed overview on identification challenges of key species in the ICES zooplankton time series from the North Atlantic and adjacent seas. Examples are given across all relevant groups, including copepods, gelatinous plankton, and meroplanktonic larvae. The high prevalence of challenging species complexes underscores the need to further explore the implications of an accurate species assignment for understanding what defines a species’ role in an ecosystem. This review highlights the dynamic nature of taxonomy, with species being split and cryptic species eventually becoming morphologically distinguishable. It provides examples showing that relying solely on molecular methods without deep taxonomic expertise poses significant risks. It also aims to serve as a starting point for delving deeper into the taxonomy of the ICES zooplankton time series.