<jats:title>Abstract</jats:title><jats:p>Ocean acidification is expected to have detrimental consequences for the most abundant calcifying phytoplankton species<jats:italic>Emiliania huxleyi</jats:italic>. However, this assumption is mainly based on laboratory manipulations that are unable to reproduce the complexity of natural ecosystems. Here,<jats:italic>E. huxleyi</jats:italic>coccolith assemblages collected over a year by an autonomous water sampler and sediment traps in the Subantarctic Zone were analysed. The combination of taxonomic and morphometric analyses together with<jats:italic>in situ</jats:italic>measurements of surface-water properties allowed us to monitor, with unprecedented detail, the seasonal cycle of<jats:italic>E. huxleyi</jats:italic>at two Subantarctic stations.<jats:italic>E. huxleyi</jats:italic>subantarctic assemblages were composed of a mixture of, at least, four different morphotypes. Heavier morphotypes exhibited their maximum relative abundances during winter, coinciding with peak annual TCO<jats:sub>2</jats:sub>and nutrient concentrations, while lighter morphotypes dominated during summer, coinciding with lowest TCO<jats:sub>2</jats:sub>and nutrients levels. The similar seasonality observed in both time-series suggests that it may be a circumpolar feature of the Subantarctic zone. Our results challenge the view that ocean acidification will necessarily lead to a replacement of heavily-calcified coccolithophores by lightly-calcified ones in subpolar ecosystems, and emphasize the need to consider the cumulative effect of multiple stressors on the probable succession of morphotypes.</jats:p>