Six populations of seeds of the aquatic monocotyledon Stratiotes (Hydrocharitaceae) from the Paleogene of England have been studied to assess morphological evolution through the Eocene–Oligocene transition. Morphometric methodologies (including eigenshape analysis) have been used to quantify evolution within the genus and compare results to previous qualitative studies. Previously hypothesized broad evolutionary trends of increasing size and more elongate shape are found to be mainly correct, but, in places, can be elucidated further. The results of this study indicate a single evolving lineage in the Paleogene of southern England with an increase in seed size and keel width in late Eocene specimens, followed by a reversal of this trend in the early Oligocene. Two Miocene populations from continental Europe are shown to be morphologically distinct from those of the English Paleogene. Changes in overall shape of the seed are shown to be controlled dominantly by the relative size of the keel structure, rather than the seed body. Comparisons show that the microevolutionary trend of Stratiotes across the Eocene–Oligocene transition differs from that of the charophyte, Harrisichara. This may suggest that factors other than climatic change, such as animal/plant interactions, played a role in evolution of Stratiotes seeds. Type and figured material of named Paleogene species was added passively to the dataset, and results suggest that taxonomic splitting may have led to previous evolutionary hypotheses of multiple clades, which is not supported by this study.