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Abstract Background The rate of anthropogenic biodiversity loss far exceeds the background rate of species extinctions. Global targets for biodiversity acknowledge this, nevertheless progress towards targets has been poor. There is now a reasonable understanding of what human pressures threaten the survival of species. However, information on where these threats are impacting species is needed to coordinate conservation actions and threat abatement efforts. Herein, threats are defined as human-driven pressures specifically where they co-occur with, and threaten the survival of, native wild species. There is a large number of studies that map either distributions of threatened species or human-driven pressures alone. This makes it difficult to identify research that has investigated the spatial distribution of the threats themselves. Additionally, the high variability in approaches taken in these studies promotes a high risk of duplication and diversity among the findings. This variation, and the lack of studies directly mapping threats, limits the utility of threat mapping studies for conservation planning and informing policy. Therefore, a systematic consolidation of the literature is necessary to identify where knowledge is lacking, and where sufficient evidence exists for synthesis of the collective findings. Methods This protocol details the process for a systematic mapping exercise aiming to identify studies that map threats to species across the world. For a study to be included it should present spatially explicit data on both the occurrence of species and the human-driven pressures threatening them. A range of peer-reviewed and grey literature repositories will be searched in English for literature published 2000–2020, followed by one iteration of backward snowballing. A three-stage screening process will be implemented before data are extracted on geographic coverage, taxonomic extent, and threats investigated. Data on the threats studied will be categorised using the threat classification scheme used by the IUCN Red List to allow comparisons among studies and to identify unrepresented threats. The extracted data will be analysed and visualised to describe the extent of existing knowledge. The resulting database of studies, findings from descriptive analyses, and accompanying narrative synthesis, will be made publicly available.