The emergence of highly pathogenic avian influenza viruses (HPAIV) has caused widespread mortality wildlife globally. In 2023, mass mortalities of southern elephant seals Mirounga leonina were observed in South America, and the virus subsequently reached the sub-Antarctic, affecting multiple species. The remoteness of these islands has limited assessment of its true impact. Here we present evidence of HPAIV´s effect on the number of breeding females at the world´s largest southern elephant seal population at South Georgia. Following the virus´ arrival in 2023, we recorded a 47% (SD = 14.2%) decline in the number of breeding females at the three largest breeding colony beaches in 2024 compared to 2022. The apparent loss of nearly half the breeding female population has serious implications for recruitment and future stability of the population. These findings highlight the urgent need for continued, intensive monitoring to track the long-term effects on this species.