With the exception of the diatoms, little is known of the extinction, colonization, and succession of marine floras during glacial cycles. Here we study both morphological and biochemical fossils in two sediment cores from the Antarctic to unravel the sequence of events over a single glacial cycle. The cores, from the nearshore continental shelf off the Windmill Islands (66°S, 110°E), east Antarctica, span the period from Marine Isotope Stage 3 or earlier to the present. New high-performance liquid chromatography and mass spectrometry methods were used to study fossil pigments with additional data from siliceous microfossils, lithological analyses, and radiocarbon dates. Results show two response processes. First, there is the large-scale impact of the expanding ice sheet in removing the flora from the inner shelf, primarily through the denial of light, destabilization of the substratum, and elimination of habitats. Second, there are a number of glacial climate interactions that have a surprisingly strong influence on recolonization and succession. These include sea ice extent and the proximity of the ice edge, the annual duration of open water, the stabilization of the substratum first by benthic diatoms and later by macrophyte algae, and relative sea level. A period of warmer climate in the mid-Holocene had a considerable influence on the composition and species diversity of the marine flora. These are the first data on the timing of colonization and succession of marine floras over a glacial cycle based on both morphological and biochemical fossils.