Fragilariopsis kerguelensis is one of the most abundant diatoms in the sediments of the Southern Ocean. Its morphometric features have been proposed as proxies, based on links with, for example, iron availability, sea surface temperature and glacial/interglacial conditions. We investigated morphometric changes in F. kerguelensis valves in a well-studied sediment core record, focusing on transition periods between glacials and interglacials. By applying a high-throughput diatom imaging and morphometry workflow, we found two clearly distinct morphotypes which were differentiated by their rectangularity. One of them occurred preferentially in glacial samples, whilst the other persisted throughout. This indicates that their relative abundances depend on environmental conditions and thereby points to the possibility that paleo-proxies based on F. kerguelensis valve morphometric features might in the future benefit from differentiating these two morphotypes. As an initial exploration of this idea, we show that the abundance ratio of both morphotypes correlates well with paleo-temperatures which had been reconstructed using independent data from the same core. Distinguishing between the two morphotypes only became possible by image analysis for precisely measuring diatom valve outlines and area, highlighting the potential of such methods for diatom analyses.