This dataset contains biomarker data (fatty acids, highly branched isoprenoids, and sterols) from six sediment cores collected during two cruises in 2014/2015 (ANA04C, ANA05B) along a transect in the southwestern Ross Sea. Three sediment cores were sampled at 0-1 cm only, while the remaining three were subsampled at various depths between 1 and 56 cm, covering approximately the last 200 years based on a 210Pb dating model. Also reported are measurements of total organic carbon, and total nitrogen, as well as diatom assemblage data, including total abundance and relative species or group level concentrations.