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Antarctica is one of the most susceptible regions to climate change on Earth. Rising ocean temperatures, glacier melting, and disruptions of marine ecosystems make this polar region a focus of research on ecosystem transformation associated with ongoing climate change. Within the Antarctic ecosystem, diatoms, a key group of phytoplankton at the base of the marine food web, play a crucial role in maintaining marine ecosystem balance and functioning. Conventionally, fossil diatom assemblages have been investigated in marine sediment records to reconstruct paleoenvironmental conditions and understand climate change patterns of Antarctica. Recently, the application of ancient DNA techniques to ocean sediments (sedimentary ancient DNA, sed aDNA) has provided new insights into diatom community responses to environmental change over geological time scales. One benefit of sed aDNA analysis is that this technique can detect fragile diatom species that do not preserve well and are thus difficult to study via traditional microscopy techniques. In this paper, we review the importance of diatoms as indicators of Antarctic paleoenvironmental change, the novel use of diatom sed aDNA to assist Antarctic paleoenvironmental reconstruction, and the challenges and promises of using the sed aDNA approach. We propose that Fragilariopsis cylindrus , an extant polar diatom species, is an ideal model organism to study adaptation patterns of diatoms to changing climate due to its ecological success through time and the availability of whole-genome information for this species. Novel genetic information obtainable from ancient F. cylindrus, as well as other diatoms, will help us to better predict the evolutionary and adaptive dynamics of this important group of primary producers in the climatically vulnerable Antarctic region. • Climate change in Antarctica and the need to study this polar region. • Diatoms in Antarctic ecosystem and their role as paleoenvironmental indicators. • Using the novel technique of sedimentary ancient DNA (sed aDNA) in Antarctica. • Fragilariopsis cylindrus to study adaptation and evolution of diatoms in Antarctica. [ABSTRACT FROM AUTHOR]