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The Galápagos Archipelago is a globally significant biodiversity hotspot. However, compared to the relatively well-known megafauna, the distribution and ecological significance of marine protists in this system are poorly understood. To gain an understanding of the protistan assemblages across trophic modes, an intensive oceanographic survey was conducted in the Galápagos Marine Reserve (GMR) in October of 2018. The Equatorial Undercurrent (EUC)-influenced region had higher chlorophyll- a (Chl- a ) concentrations than those of the eastern regions of the archipelago, along with higher abundances of protistan grazers. Specifically, proportions of autotrophic and potentially mixotrophic dinoflagellates were higher in the EUC, whereas in the eastern regions, heterotrophic dinoflagellates and chlorophytes dominated. Taxonomic composition and biochemical indicators suggested proportions of micrograzers and their associated heterotrophic biomass was higher in the oligotrophic, low Chl- a regions in the east. We also report observations from a dinoflagellate bloom in the western archipelago, which was heavily influenced by upwelling of the EUC. The red tide-forming dinoflagellate Scrippsiella lachrymosa was highly detected through light microscopy and DNA amplicon sequencing. In addition, the heterotrophic dinoflagellate Polykrikos kofoidii was detected and, based on cell densities observed in this study and grazing rates obtained from the literature, estimated to potentially graze up to 62% of S. lachrymosa bloom population. Our findings thus provide new insights into the composition of micrograzers and their potential roles in structuring protistan communities in the Galápagos Archipelago. 

ABSTRACT The Galápagos Islands are a biodiversity hotspot, largely due to the Equatorial Undercurrent (EUC) which supplies nutrient‐rich waters to the euphotic zone and supports enhanced levels of primary productivity performed by phytoplankton. Understanding phytoplankton responses to changing environmental conditions is crucial for regional conservation and management efforts. Research cruises conducted between 2014 and 2022, spanning a major El Niño event in 2015 and a La Niña event in 2022, observed varying oceanic conditions and diverse phytoplankton community composition. At most EUC‐influenced stations, larger‐sized phytoplankton groups (≥ 5 μm) were dominant while warmer, oligotrophic sites favoured smaller‐sized phytoplankton groups (< 5 μm). Predictably, nutrient supply was suppressed during the El Niño event associated with the weakening of the EUC and deepening of the thermocline. Counterintuitively, nutrient levels were not significantly enhanced during the La Niña event likely because increased stratification between the mixed and deep water layers reduced entrainment, particularly at Eastern stations. Protist community composition was evaluated using 18S rRNA gene metabarcoding; the majority of detected OTUs were associated with upwelling conditions prevalent around the archipelago. Taxonomic variability reflected heterogeneous environmental conditions generated by the convergence of multiple ocean currents. These results highlight the dynamic interplay of physical and biological factors shaping primary productivity in the Galápagos marine ecosystem.