Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. In this work, we use DNA metabarcoding of 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem. The PITs included formalin-fixed and 'live' traps to investigate compositional changes associated with consumption and remineralization processes. Sequences affiliated to Radiolaria, mainly Spumellaria and Acantharia, dominated the eukaryotic assemblage in fixed-traps (90%) with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased markedly in live-traps (<3%), possibly due to selective consumption by large copepods, heterotrophic nanoflagellates and amoeboid phaeodarians that were heavily enriched in these traps. These patterns were consistent across the coastal-to-open water masses surveyed, despite major differences in productivity and trophic structure of the epipelagic plankton community. Our findings indicate that in addition to more commonly considered phytoplankton and crustacean zooplankton, the role of rhizarians can be significant for POM vertical export and cycling in the CCE and potentially in other oceanic ecosystems.