<jats:title>Abstract</jats:title><jats:p>Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the <jats:italic>Peronosporaceae</jats:italic>—one could be assigned to <jats:italic>Peronospora verna</jats:italic>, an obligate biotrophic pathogen of the terrestrial plant <jats:italic>Veronica serpyllifolia</jats:italic> and related species, the other was closely related to <jats:italic>Globisporangium rostratum</jats:italic>. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the <jats:italic>Peronosporaceae</jats:italic> are known to withstand high salt concentrations. Two OTU lineages could be assigned to the <jats:italic>Saprolegniaceae</jats:italic>. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of <jats:italic>cox</jats:italic>2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.</jats:p>