The vertical distribution of phytoplankton standing crop, number of species, and community diversity in five transects across the ecotone of the Antarctic Convergence were studied in relation to physical and chemical habitat variables (light, temperature, salinity, density, relative stability, oxygen, phosphate, nitrate, and silicate) and to bacteria and yeasts. Two distinct phytoplankton communities were observed, one north and one south of the convergence. Within the convergence the southern diatomaceous Antarctic community sinks with the formation of Antarctic Intermediate Water and can be traced underneath the northern dinoflagellate subantarctic community by use of indicator species. Chaetoceros bulbosum, Chaetoceros dichaeta, Dactyliosolen antarctica, and Eucampia zoodiacus were used as indicators of the Antarctic community, and Rhizosolenia delicatula, Amphidinium amphidinoides, Oxytoxum variabile, and Phalacroma pulchellum represented the subantarctic community. Submergence of the Antarctic community is corroborated by the vertical distribution of phytoplankton biomass. South of the convergence in the upwelling system, biomass maxima of the phytoplankton consist of Antarctic species. Within the convergence separate subsurface biomass maxima contain the Antarctic community, and both Antarctic and subantarctic species constitute surface maxima of standing crop. In the upper water of the oceanic system north of the convergence, subantarctic species make up most of the biomass, where as small numbers of Antarctic species were observed in the aphotic zone. Surface layers of the euphotic zone in both systems were dominated by a small number of species. Maxima of species number occurred deeper than those of biomass, possibly reflecting the result of competitive exclusion. A low community diversity was observed in the upper water of each area, and a high ecotonal diversity was found at the convergence. A linear multiple regression analysis showed the relative importance of habitat variables in predicting the vertical distribution of the phytoplankton both within the oceanic and upwelling systems and within their transition zone. Water—mass structure, turbulence, light, silicate, and an index of heterotrophic conditions can be used to predict up to 66% of phytoplankton variation across the convergence. Additional prediction can only be achieved by incorporation of biological rate data and nonlinear expression of variable interaction in simulation models based on the present analysis.