The coastal oceans can be highly variable, especially near ocean fronts. The Ushant Front is the dominant oceanographic feature in the Iroise Sea (NE Atlantic) during summer, separating warm stratified offshore waters from cool vertically-mixed nearshore waters. Mesozooplankton community structure was investigated over an annual cycle to examine relationships with oceanographic conditions. DNA metabarcoding of COI and 18S genes was used in communities from six sites along two cross-shelf transects. Taxonomic assignments of 380 and 296 OTUs (COI and 18S, respectively) identified 21 classes across 13 phyla. Meroplankton relative abundances peaked in spring and summer, particularly for polychaete and decapod larvae, respectively, corresponding to the reproductive periods of these taxa. Meroplankton was most affected by season, while holoplankton varied most by shelf position. Copepods with a mixed feeding strategy were associated with the most offshore sites, especially in the presence of the front, while filter-feeding or carnivorous copepods were associated with nearshore sites. In sum, mesozooplankton communities in well-mixed coastal waters were distinct from those found in the Ushant Front (high thermal stratification and chlorophyll-a). Furthermore, the benthic compartment, through its partial life cycle in the water column, contributed to high heterogeneity in planktonic communities over short temporal and spatial scales.