This dataset contains coccolithophore abundance data from CTD bottle samples collected during the AMT15 cruise in the Atlantic between the United Kingdom and Cape Town, South Africa in September-October 2004. Bottle samples were collected from 6 light depths from the pre-dawn (between approximately 03:00 - 04:30 local time) and noon CTD casts. Microscope enumeration of coccolithophores and coccoliths was performed by filtering a 100 - 500 millilitre water sample through a Millipore HA filter, which was then rinsed with borate buffer, and frozen in a petri dish until counted. The filter was placed on a glass microscope slide, and a 60 degrees Celsius Canada Balsam was placed on top of the filter, followed by a cover slip. The clarified filter was examined for birefringent and plated coccolithophore counts, with an Olympus BH2 microscope equipped with polarisation optics. For statistical reasons, 200 coccoliths or cells were counted from each sample, when available. These data were collected for the Atlantic Meridional Transect (AMT) project by scientists from the Bigelow Laboratory for Ocean Sciences.