Escalating anthropogenic threats to the Atlantic Forest, a renowned biodiversity hotspot, has placed the region in the spotlight for current conservation efforts. Faunal overexploitation and habitat degradation are among key factors driving the region’s recent declines in faunal populations and biodiversity. Assessing the scale of these impacts is complicated by the near-complete absence of historical reference baselines. In this paper, Thiago Fossile and colleagues offer a contribution to bridge this knowledge gap by analysing faunal remains from two historical archaeological sites, Morro Grande 1 (MG1) and Praia Grande Unidade 21 (PG-U21), in Babitonga Bay (Santa Catarina state, Brazil) dated between 1750 to 1950 AD. This study provides compelling evidence that the selective hunting of medium- and large-bodied native terrestrial mammals has persisted in the region for over 4500 years, and requires us to reconsider the idea of a heavy reliance on domestic animals during early European colonisation of southern Brazil. Our study thus traces the causes of regional terrestrial mammal defaunation back to the Pre-colonial and Historical times. We recommend the integration of historical and archaeological data into modern faunal population assessments and conservation initiatives to set more informed reference baselines.