Here, we present datasets of diatom abundance and a diatom-based sea surface temperature reconstruction from the Iceland Basin. The 419.5 cm long marine sediment core DA12-11/2-GC01 was recovered in September 2012 by the Danish R/V Dana using a gravity corer. The core was taken from a location at the northern edge of the Gardar Drift and the eastern edge of the Björn Drift in the Iceland Basin (61.36.536 °N, 20.42.164 °W) at a water depth of 2120 m. Diatoms were analysed at 5 cm intervals over the upper 2 m of core, representing the period 6100-0 cal years BP, with chronological constraints provided by 6 radiocarbon dates. Diatoms were analysed using standard procedures, including the identification and counting of a minimum of 300 diatom per sample, which allowed calculation of the percentage abundances of different species. These abundances were converted into estimates of sea surface temperature using the weight averaging partial least squares transfer function approach.