AbstractA quantitative understanding of the mesopelagic zooplankton food web is key to development of accurate carbon budgets and geochemical models in marine systems. Here we use compound specific nitrogen stable isotope analysis of amino acids to quantify the trophic structure of the microzooplankton and mesozooplankton community during summer in the subarctic northeast Pacific Ocean during the EXport Processes in the Ocean from Remote Sensing (EXPORTS) field campaign. Source amino acid values in particles and zooplankton provide strong evidence that basal resources for the mesopelagic zooplankton food web were primarily small (), suspended or slow‐sinking particles, but that surface organic matter delivered by vertically migrating zooplankton may have also been important. Comparisons of values of source and trophic amino acids provide estimates of food web length, which decrease significantly with depth and suggest that protistan microzooplankton are key components of the food web from the surface to at least 500. These results emphasize the importance of small particles as a source of carbon and nitrogen to mesopelagic communities in this region, support observations of an inverse relationship between zooplankton vertical migration and small particles as sources of carbon to deep‐sea food webs in low productivity environments, and document the role of heterotrophic protists as key trophic intermediaries in the mesopelagic zone at this location.