High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a</p><p>significant proportion of which remains uncharacterized. Here we use a temporal approach to</p><p>understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-</p><p>throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus</p><p>and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our</p><p>ability to track OTUs temporally to evaluate the ability of 18S sequence-based OTU assignments</p><p>to meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic in</p><p>terms of both species richness and composition, though proportional representation of higher-</p><p>order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughout</p><p>the year. This study has resulted in a temporal dataset of eukaryotic 18S sequences that cover a wide range of taxa and offers insights into the pier microbial community and how it changes with time.