Relevant baselines on the historical distribution of species are needed to support appropriate conservation targets for depleted species. In South Africa, over-hunting and loss of habitat largely altered the composition and distribution of the large mammal fauna, especially since the start of the colonial period. Using modern ecological data therefore has the risk of considerably underestimating the full scale of anthropogenic impacts on biodiversity. By extending the timeline usually considered in ecology, long-term archives can provide novel insights into changing species distributions through time and represent a unique opportunity to better inform regional environmental management. Here, we use a large dataset of past distribution records for medium- to large-sized terrestrial mammals in South Africa, assembled from sources of the early historical period (late 1400s to the 1920s) to reconstruct the historical extent of occurrence and extinction dynamics for >30 large mammal species. We evidence local extinctions and changes in community composition since the early historical period. The biogeography of population loss is consistent with a response to the demographic expansion of European colonists spreading from the south-western part of South Africa. These results contribute to novel baselines for conservation and provide a strengthened evidence-base for understanding long-term faunal responses to human pressures. These findings also allow the "shifted baselines" around modern mammal distributions to be identified, providing an avenue for new analyses of large mammal biogeographic patterns for this region.