Abstract South American fur seals (Arctocephalus australis) are widely distributed, yet surprisingly little is known about their ecology. In particular, population data are sparse and outdated for many breeding locations, including the Falkland Islands. Data deficiency impedes the development of coherent conservation and management strategies. To address knowledge gaps, for the first time since 1965 an archipelago‐wide census of South American fur seals breeding at the Falkland Islands was undertaken, which provided the first pup abundance estimate since 1926 – data that are critical for assessing population trends. In total, 36,425 South American fur seal pups were counted at the Falkland Islands in 2018, a greater than four‐fold increase since the last census, and far greater than the 7,990 pups counted in Uruguay, which was presumed to be the largest South American fur seal population in the world. Hence, based on pup abundance, the Falkland Islands is presently the largest population of South American fur seals, even when considering a correction factor of 3.9 that was applied to pup counts in Uruguay, which yielded an estimated 31,160 pups. The results redefine South American fur seal abundance, the contribution of breeding locations (Falkland Islands, Uruguay, Argentina, Chile) and the distribution of breeding colonies at the Falkland Islands, which has far reaching implications for conservation and management. In particular, the present study has effectively doubled the Atlantic population size of the species, which is now estimated to comprise about 76,000 pups, of which the Falkland Islands accounts for 48% and Uruguay 41%. Accordingly, changes in the number of South American fur seals breeding at the Falkland Islands will influence the global population trends and conservation status of the species. Monitoring South American fur seals breeding at the Falkland Islands is therefore crucial to understand the impacts of anthropogenic pressures, such as fisheries, and to inform management and conservation policy. The results provide a baseline from which to measure changes in abundance.