Radiolaria and Phaeodaria are single-celled eukaryotic zooplankton that inhabit diverse marine environments. While the sedimentary fossil record reveals their ancient origins and morphological diversity, recent advancements in metagenomics and sedimentary ancient DNA (sedaDNA) techniques have highlighted the significant contributions of rarely preserved taxa (e.g., those that are only lightly silicified or soft-bodied) to marine biodiversity and the carbon cycle. Using a paleo-genomic approach, we produced a sedaDNA-based time series of the Radiolarian and Phaeodarian community from the Scotia Sea covering the last 500 kyr. We compared the use of two reference databases, one Radiolarian- and Phaeodarian-specific (RPD) and one more comprehensive eukaryote database (PR2), to assess the validity of a small, taxa-specific database. We determined that the two databases produced comparable results, showing that the overall assemblage changes at the glacial-interglacial scale were similar. At the Class level, Radiolarian and Phaeodarian assemblages appear to have experienced compositional changes during termination events and warm Interglacial periods. This study produced the first Radiolarian- and Phaeodarian-specific reference database. We showed that the Class-level changes that occurred over the last 500 kyr were associated with glacial-interglacial (G-I) cycles, and no permanent shifts away from the natural variation associated with the G-I cycles were found.