Bioregionalisation, the partitioning of large ecosystems into functionally distinct sub-units, facilitates ecosystem modelling, management and conservation. A variety of schemes have been used to partition the Southern Ocean, based variously on frontal positions, sea ice, productivity, water depth and nutrient concentrations. We have tested the utility and robustness of ecosystem bioregionalisation for the Scotia Sea, by classifying spring, summer and autumn stations on the basis of nutrient concentrations, phytoplankton taxa, meso- and macrozooplankton, fish catches and acoustic data. Despite sampling across different seasons and years, at different spatial scales and taxonomic resolutions, cluster analysis indicated basically consistent spatial divisions across this wide range of trophic levels. Stations could be classified into two main groups, lying broadly to the north and south of the Southern Antarctic Circumpolar Current Front (SACCF). In some aspects the 2 station groups were similar, with both having variable but often high phytoplankton biomass as well as similar biomass of fish. However, the colder water southern group, most of which was covered by seasonal sea ice, had a fundamentally different food web structure to that in the northern Scotia Sea. The cold water community had a depleted, cold-adapted fauna characterised by low zooplankton biomass, Euphausia superba and the fish Electrona antarctica and Gymnoscopelus braueri. In contrast the northern group was richer with higher mesozooplankton biomass and a fauna of warmer or more cosmopolitan species such as Themisto gaudichaudii, Euphausia triacantha and the fish Protomyctophum bolini, Kreffticthys anderssoni and Gymnoscopelus fraseri. The position of the food web transition, broadly consistent with the position of the SACCF, supports a recent circumpolar-scale bioregionalisation. However, there is little evidence that this relatively weak frontal transition represents a significant barrier either here or elsewhere in the Southern Ocean. We suggest that broader-scale factors, namely temperature and possibly the extent of the seasonal ice-zone, within which most of the southern stations lay, were more likely to influence biological zonation.