Reliable records of Southern Ocean seawater palaeotemperatures are important because this region plays a significant role in regulating global climate change. Biomarkers such as GDGT-based indices have been effectively used to reconstruct seawater temperatures. We analysed the composition and distribution of iGDGTs, OH-GDGTs and brGDGTs and calculated GDGT-based temperature indices in surface sediments from Prydz Bay, East Antarctica. Our results showed that iGDGTs, OH-GDGTs and brGDGTs are all produced in situ, with iGDGTs and OH-GDGTs mostly synthesized by Thaumarchaeota. Concentrations of iGDGTs, OH-GDGTs and brGDGTs showed similar spatial distributions and decreased from the continental shelf towards the deep ocean. The highest concentrations were in the inner bay, which is attributed to a combination of (1) bathymetry that reduces water exchange, (2) the Prydz Bay Gyre stabilizing the upper water column and (3) sea ice that releases archaea and bacteria. Among the temperature indices based on iGDGTs, OH-GDGTs and combinations therein, those based on OH-GDGTs showed the strongest correlation with seawater temperature. Some OH-GDGT-based indices (e.g., OH-0/OHs, OH-1/OHs, OH-2/OHs and RI-OH′) exhibited a stronger correlation with annual subsurface ocean temperature (100–200 m), which may be related to archaeal habitats and production mechanisms. Our study suggests that RI-OH′ and OH-0/OHs could be used as indicators of annual subsurface ocean temperature in Antarctic marginal seas.