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Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific (33–58° S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises (n= 482, 0–3100 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) surface water masses and the Subtropical Front (STF) that separates them. Diversity decreased with increasing latitude and increasing temperature but tended to be lowest in the STF. Sample …