Although world oceans have been warming over the past 50 years, the impact on biotic components is poorly understood because of the difficulty of obtaining long-term data sets on marine organisms. The Southern Ocean plays a critical role on global climate and there is growing evidence of climate warming. We show that air temperatures measured by meteorological stations have steadily increased over the past 50 years in the southern Indian Ocean, the increase starting in mid 1960s and stabilizing in mid 1980s, being particularly important in the in the sub-Antarctic sector. At the same time with a time lag of 2–9 years with temperatures, the population size of most seabirds and seals monitored on several breeding sites have decreased severely, whilst two species have increased at the same time. These changes, together with the indications of a simultaneous decrease in secondary production in sub-Antarctic waters and the reduction of sea-ice extent further south, indicate that a major system shift has occurred in the Indian Ocean part of the Southern Ocean. This shift illustrates the high sensitivity of marine ecosystems, and especially upper trophic level predators, to climate changes.