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The community structure of pelagic zooplankton and micronekton may be a sensitive indicator of changes in environmental conditions within the California Current ecosystem. Substantial oceanographic changes in 2015 and 2016, due to the anomalously warm ocean conditions associated with a large-scale marine heatwave perturbation, resulted in onshore and northward advection of warmer and more stratified surface waters resulting in reduced upwelling. Here we quantify changes in the macrozooplankton and micronekton community composition and structure based on five highly contrasting ocean conditions. Data from fine-mesh pelagic trawl surveys conducted off Oregon and Washington during early summer of 2011 and 2013-2016 were examined for interannual changes in spatial distribution and abundance of fish and invertebrate taxa. Overall species diversity was highest in 2015 and lowest in 2011, but 2016 was similar to the other years, although the evenness was somewhat lower. The community of taxa in both 2015 and 2016 was significantly different from the previously sampled years. Crustacean plankton densities (especially Euphausiidae) were extremely low in both of these years, and the invertebrate composition became dominated mostly by gelatinous zooplankton. Fishes and cephalopods showed mixed trends overall, but some species such as age-0 Pacific hake were found in relatively high abundances mainly along the shelf break in 2015 and 2016. These results suggest dramatically different pelagic communities were present during the recent warm years with a greater contribution from offshore taxa, especially gelatinous taxa, during 2015 and 2016. The substantial reorganization of the pelagic community has the potential to lead to major alterations in trophic functioning in this normally productive ecosystem.