The Southern Ocean is experiencing rapid and profound changes in its physical and biogeochemical properties that may influence the distribution and composition of pelagic plankton communities. Coccolithophores are the most prolific carbonate-producing phytoplankton group, playing an important role in Southern Ocean biogeochemical cycles. However, knowledge is scarce about the record of (sub-)fossil coccolith assemblages in the Southern Ocean, which constitute invaluable indicators for palaeoenvironmental reconstructions. This study investigates coccolith assemblages preserved in surface sediments of southernmost Chile and across the Drake Passage that were retrieved during R/V Polarstern expedition PS97. We focused on the coccolith response to steep environmental gradients across the frontal system of the Antarctic Circumpolar Current and to hydrodynamic and post-depositional processes occurring in this region. We used statistical analyses to explore which environmental parameters influenced the coccolith assemblages by means of cluster and redundancy analyses. We specifically assessed the morphological diversity of the dominant taxa, i.e. Emiliania huxleyi, emphasizing biogeographical variability of morphotypes, coccolith sizes and calcite carbonate mass estimations. High coccolith abundances and species diversity compared to studies in the same area and in other sectors of the Southern Ocean occur, with a high species richness especially south of the Polar Front. While the surface sediments offshore Chile and north of the Polar Front provide suitable material to reconstruct overlying surface ocean conditions, further factors such as temporary thriving coccolithophore communities in the surface waters or transport of settling coccoliths via surface and bottom currents and eddies influence the (sub-)fossil coccolith assemblages south of the Polar Front. Additionally, deeper samples in the southern part of the study area are particularly affected by selective carbonate dissolution. We identified five E. huxleyi morphotypes (A, A overcalcified, R, B/C and O) and estimated coccolith carbonate masses on the basis of scanning electron microscope images. E. huxleyi morphologies reflect diverging biogeographical distributions, trending towards smaller and lighter coccoliths to the south and emphasizing the importance of documenting those morphologies in relation to changing environmental conditions to assess their response to projected environmental change in the Southern Ocean.