A sediment core from Progress Lake, one of the oldest lacustrine sequences in East Antarctica, contains distinct zones dating from a previous interglacial (most likely Marine Isotope Stage 5e, c. 125–115 kyr BP) and the present interglacial (Marine Isotope Stage 1), separated by a transition zone representing when the lake became sub-glacial. Profiles of fossil pigments, determined using high performance liquid chromatography and liquid chromatography-tandem mass spectrometry, show distinct differences in the photoautotrophic community during these two interglacial periods. The first was dominated by algae and purple phototrophic bacteria, with periods of photic zone euxinia indicated by pigments from anoxygenic phototrophic bacteria. Specific chlorophyll a derivatives reveal periods when grazing pressure impacted significantly on the phytoplankton community. The virtual absence of pigments in the transition zone reflects severe restriction of photoautotrophic activity, consistent with the lake having become sub-glacial. Retreat of snow and ice in the late Holocene (3345 14C yr BP) allowed establishment of a less diverse primary producer community, restricted to algae and cyanobacteria. Grazers were severely restricted and oxidative transformation was more important than during the previous interglacial. The pigment data provide a unique and detailed insight in to the evolution of the lake ecology over an interglacial-glacial-interglacial transition and strong evidence that the Marine Isotope Stage 5e interglacial in this region of coastal East Antarctica was several degrees warmer than at present.