Summary We performed a metagenomic survey (6.6 Gbp of 454 sequence data) of S outhern O cean ( SO ) microorganisms during the austral summer of 2007–2008, examining the genomic signatures of communities across a latitudinal transect from Hobart (44° S ) to the M ertz G lacier, A ntarctica (67° S ). Operational taxonomic units ( OTUs ) of the SAR 11 and SAR 116 clades and the cyanobacterial genera P rochlorococcus and S ynechococcus were strongly overrepresented north of the P olar F ront ( PF ). Conversely, OTUs of the G ammaproteobacterial S ulfur O xidizer‐ EOSA ‐1 ( GSO‐EOSA ‐1) complex, the phyla B acteroidetes and V errucomicrobia and order R hodobacterales were characteristic of waters south of the PF . Functions enriched south of the PF included a range of transporters, sulfur reduction and histidine degradation to glutamate, while branched‐chain amino acid transport, nucleic acid biosynthesis and methionine salvage were overrepresented north of the PF . The taxonomic and functional characteristics suggested a shift of primary production from cyanobacteria in the north to eukaryotic phytoplankton in the south, and reflected the different trophic statuses of the two regions. The study provides a new level of understanding about SO microbial communities, describing the contrasting taxonomic and functional characteristics of microbial assemblages either side of the PF .