This micropalaeontological dataset includes morphometries of the extant coccolithophore species Emiliania huxleyi in two transects in the Pacific sector of the Southern Ocean (from New Zealand to Antarctica and across the Drake Passage). The Drake Passage transect: 19 water samples were collected on a transect at the western end of the Drake Passage (55.44°S to 61.75°S) during Polarstern Expedition PS97 from 24th February 2016 to 5th March 2016. The shallowest CTD water samples (retrieved at 5, 10 and 20 m water depth) were considered in this study. A total of 203 E. huxleyi coccoliths were classified and measured using SEM images.