Fragilariopsis kerguelensis (O’ Meara) Hust. is a ubiquitous diatom of the Southern Ocean. Its thick frustules are the numerically dominant component of the siliceous sediment layer covering large parts of the seafloor beneath. Morphometric variability of frustules of this diatom has been of interest for paleoenvironmental reconstructions. Recently, two morphotypes differentiated by the morphometric descriptor rectangularity were described from a Southern Ocean sediment core, the relative abundance of which correlated with reconstructed paleotemperatures. In the present study, we use semi-automated microscopic and image analysis methods to answer whether these morphotypes also appear in recent assemblages, and if yes, do their distributions reflect geographic location or environmental factors. Three transects from the water column, sampled along the Greenwich meridian with hand nets, and one sediment surface transect from the South Pacific, were analyzed. In each of these transects, both morphotypes were detected, and annual mean sea surface temperatures (SST) were found to be a good predictor of their relative abundances. The transition between dominance of one or the other morphotype appeared roughly between the Antarctic Polar Front and the Southern Boundary of the Antarctic Circumpolar Current. Although more extensive circumpolar sampling will be needed to confirm the generality of our conclusions, the observed morphometric cline is a novel aspect of the biology of this species and can in the future potentially be used for further developing paleoproxies especially for highly F. kerguelensis-dominated sediment in the Southern Ocean.