Changing climate is causing shifts in community composition and diversity of marine microalgal assemblages, especially in coastal ecosystems. Molecular techniques enable rapid characterisation of eukaryotic microalgal communities (EMCs), however, many geographic regions still lack baseline assessments of EMC structure and composition. Our study uses environmental DNA metabarcoding of the ribosomal DNA 18S-V9 gene region and bioinformatics to characterise EMCs across a latitudinal gradient from the South Pacific to the Ross Sea, Antarctica. High-level taxonomic divisions were used to assess overarching trends within and among EMCs. The temperate ecoregion had the highest alpha-diversity, and most distinct EMC of all ecoregions. Latitudinal gradients of high-level taxonomic groups were present, with shifts from dinoflagellate dominant EMCs at lower latitudes to diatom dominant at higher. Habitat similarities, environmental conditions (homogenous selection), and close-proximity (homogenising dispersal) shaped EMCs within ecoregions, while variable conditions and selection (variable selection), and limited interconnectivity (dispersal limitation) had a greater impact on EMC structure among ecoregions. This study provides a snapshot of EMC diversity across five ecoregions, from a single season. Despite the lack of seasonal and spatial information, baseline surveys like this are crucial for predicting future EMCs and detecting community shifts in the face of future oceanic changes.