As part of two USJGOFS cruises, we investigated spatial variability in phytoplankton properties across the strong environmental gradient associated with the Antarctic Polar Frontal Zone during late austral summers of 1997 and 1998. Cell properties, including size and an index of pigment content as well as photosynthetic efficiency (as indicated by relative variable fluorescence), changed dramatically across this frontal region. A general trend toward reduced photosynthetic efficiency south of the Polar Front was correlated with low dissolved iron concentration and is consistent with physiological iron limitation in the phytoplankton. We detected no significant differences in photosynthetic efficiency among different size classes of the dominant pico- to nanophytoplankton, despite a systematic community level shift toward larger sized cells south of the Polar Front. In contrast to other cells, those classified as cryptophyte algae showed relatively high photosynthetic efficiency in low iron waters; however, this group was never found in high abundance. One group, all cells ⩽2 μm, showed an unexpected increase in intracellular pigment content (based on single cell chlorophyll fluorescence measurements) south of the Polar Front where dissolved iron concentration and the cells’ relative abundance were low. Overall, these results suggest that group- or size-specific differences in physiological status were not directly regulating community structure in the pico- to nanophytoplankton during the late summer season; other processes, such as differential grazing or sinking losses, must be important.