The ongoing expansion of highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b has resulted in unprecedented outbreaks among wild birds and marine mammals, raising concerns about viral dissemination into Antarctica. Here, we investigated fecal samples from Weddell seals (Leptonychotes weddellii) and Southern Elephant seals (Mirounga leonina) collected in Antarctica using molecular screening and whole-genome sequencing. HPAIV H5N1 clade 2.3.4.4b was detected and genetically characterized, showing evidence of viral circulation in these Antarctic pinnipeds. Phylogenetic analyses placed the virus within the South American lineage currently circulating in wild birds and marine mammals. Our findings demonstrate the usefulness of non-invasive fecal sampling for pathogen surveillance and provide further evidence that Antarctic marine mammals are exposed to the ongoing H5N1 epizootic, emphasizing the need for continued monitoring under a One Health framework.