Diatoms are important primary producers in present day Antarctic waters but their relative significance in the past is less clear. In this study we used long-chain diols to reconstruct Proboscia diatom productivity in shelf waters of the western Antarctic Peninsula over the last 8500 yr. Biomarker lipid analysis revealed the presence of a suite of long-chain diols in the sediments, mainly comprising the C28 and C30 1,14-diol isomers derived from Proboscia diatoms and C28 and C30 1,13-diols derived from other unknown algae. The relative importance of Proboscia diatoms was assessed using the relative abundances of 1,14-diols versus 1,13-diols, which showed that Proboscia diatoms were relatively more abundant during the Late Holocene, suggesting that stronger upwelling of circumpolar waters occurred at that time. The variations in the diol index strongly correlate with melt events in the Siple Dome ice core, suggesting that the climatic processes responsible for changes in mean summer temperature, open marine influence and atmospheric cyclonic activity recorded at Siple Dome, also controlled the productivity of Proboscia diatoms on the western Antarctic Peninsula region.