Diatom abundance and assemblage data are presented for JPC43 - a ~12 m marine sediment core recovered from 576 m water depth in Neny Fjord, Marguerite Bay, Antarctic Peninsula (68.2571°S, 66.9617°W). The core was collected aboard the RVIB Nathanial B Palmer in 2002 during the NBP0201 scientific cruise (PI: Prof J B Anderson) to determine the timing of deglaciation in the fjords of the Antarctic Peninsula. The core record spans the Holocene with samples dated using an age model based on 5 reliable radiocarbon dates. Diatom concentrations and the contribution of Chaetoceros resting spores (CRS %) are calculated from counts (mean=474.4 valves) of the whole diatom assemblage - 'total counts' (n=81); relative abundance of all other diatom taxa are based on counts (mean=363.1 valves) excluding CRS - 'CRS-free counts' (n=66). The relevant methods are described and referenced in the associated publication (Allen et al. 2010).