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Protists (eukaryotic microorganisms) commonly form symbiotic associations with crustacean zooplankton, but their diversity, prevalence and ecological roles are underestimated due to the limited scope of previous investigations. Using metabarcoding of the V4 region of the 18S rRNA gene, we characterized the eukaryotic microbiomes of the dominant crustacean zooplankton, specifically copepods, euphausiids, amphipods and ostracods, from the Strait of Georgia, Canada. Sequence reads from the alveolates dominated all zooplankton examined, which mostly comprised ciliates and dinoflagellates of known symbiont lineages. These lineages included not only those of parasitoids but also those of uncharacterized species. Apostome ciliate reads were the most abundant in all hosts except for cyclopoid copepods, which were dominated by the parasitic Syndiniales. Most symbiont lineages showed some degree of host preference, particularly Pseudocolliniidae ciliate parasites with ostracods, but were often detected in all hosts indicating broad host specificity. Reads from free-living protists, including diatoms and surprisingly hydrozoans, were inferred to be part of their diet. Hydrozoans may have been ingested from free organic matter, such as detritus or marine snow, suggesting a likely underestimated pathway of carbon cycling. This investigation contributes to resolving the interactions between zooplankton and protists and the potential ecological significance of symbioses on zooplankton productivity. [ABSTRACT FROM AUTHOR]