The Southern Ocean south of Australia is oceanographically complex, being characterized by double branches of the Sub-Antarctic Front (SAF), Polar Front (PF) and Southern Antarctic Circumpolar Current (SACCF), in addition to the Southern Boundary (SB) of the ACC. From 25 February to 3 March 2002 a 2150-km Continuous Plankton Recorder (CPR) transect was conducted along 140°E, between 47.02°S and 66.36°S, crossing each of these frontal zones. Surface temperature, salinity, and fluorescence were measured at 1-min intervals in conjunction with CPR samples. Additional physical data for the region south of 61°S was provided by nine CTD stations. Multivariate and Indicator Species analysis of the high resolution (~9.2 km) zooplankton samples identified six distinct assemblages which were strongly correlated with frontal/oceanographic zones. These assemblages appeared to be structured by a combination of zonal differences in water mass structure, phytoplankton regimes, and small scale intra-zonal features (e.g. eddies). The northern branch of the SAF was the strongest biogeographic boundary, separating a high proportion of sub-tropical and temperate species from the waters to its south. The study area differed from other sectors of the Southern Ocean in that the northern PF, equivalent to the PF in other sectors, was not a zone of distinct ecological transition. Two of the identified assemblages were located with the seasonal ice zone, south of the northern SACCF. Although Euphausia superba larvae were a component of both of these assemblages, this species, together with appendicularia, was most abundant south of the SB. The seasonal ice zone north of the SB was dominated by small copepods (Oithona similis and Ctenocalanus citer), appendicularia and foraminifera. Although the physical characteristics of the frontal zones can be subtle, the demarcation between zooplankton assemblages was clear. Cross-frontal changes in zooplankton assemblages highlight their role in long-term monitoring programs as indicators of environmental change.