<jats:title>Summary</jats:title><jats:p>Bacterial biogeography and activity in the Southern Ocean are poorly understood to date. Here, we applied CARD‐FISH to quantify bacterial community structure from the subtropics to Antarctica between 10°W and 10°E, covering four biogeographic provinces with distinct environmental properties. In addition, incorporation of radiolabeled glucose, amino acids and leucine via MAR‐FISH served to quantify the contribution to substrate turnover by selected bacterial groups. SAR11, <jats:italic>Bacteroidetes</jats:italic>, <jats:italic>Gammaproteobacteria</jats:italic> and the <jats:italic>Roseobacter</jats:italic> group accounted for the majority of the bacterial community (52%−88% of DAPI‐stained cells) but showed little distributional variation between provinces. In contrast, taxonomic subclades <jats:italic>Polaribacter</jats:italic>, NS5, NS2b (<jats:italic>Bacteroidetes</jats:italic>) as well as RCA (<jats:italic>Roseobacter</jats:italic> group) featured marked geographic variation, illustrated by NMDS and coefficients of variation. <jats:italic>Roseobacter</jats:italic> (specifically RCA) and <jats:italic>Gammaproteobacteria</jats:italic> constituted considerable fractions of cells incorporating glucose and amino acids respectively. <jats:italic>Bacteroidetes</jats:italic> had generally lower activities, but <jats:italic>Polaribacter</jats:italic> accounted for a major fraction of biomass production at one station near the Antarctic ice shelf. In conclusion, distributional patterns at finer taxonomic level and highest substrate turnover by less abundant taxa highlight the importance of taxonomic subclades in marine carbon fluxes, contributing to the understanding of functional bacterial biogeography in the Southern Ocean.</jats:p>