Antarctic seals and seabirds are strongly dependent on sea-ice cover to complete their life history. In polar ecosystems, sea ice provides a habitat for ice-associated diatoms that ensures a substantial production of organic matter. Recent studies have presented the potential of highly branched isoprenoids (HBIs) for tracing carbon flows from ice algae to higher-trophic-level organisms. However, to our knowledge, this new method has never been applied to sub-Antarctic species and Antarctic seals. Moreover, seasonal variations in HBI levels have never been investigated in Antarctic predators, despite a likely shift in food source from ice-derived to pelagic organic matter after sea-ice retreat. In the present study, we described HBI levels in a community of seabirds and seals breeding in Adélie Land, Antarctica. We then validated that sub-Antarctic seabirds had lower levels of diene, a HBI of sea-ice diatom origin, and higher levels of triene, a HBI of phytoplanktonic origin, compared with Antarctic seabirds. Finally, we explored temporal changes in HBI levels after the ice break up in summer. The level of diene relative to triene in Adélie penguin chicks increased and then declined during the breeding season, which was consistent with the short and intense proliferation of sea-ice algae in spring, followed by the pelagic phytoplankton bloom in summer. HBI biomarkers in Antarctic seabirds and seals thus indicate a shift from ice-algal derived organic matter to a pelagic carbon source during the summer breeding season.