Southern South American peatlands (SSAP) play a key role in the ecological dynamics of Patagonia. They mostly comprise of undisturbed environments which provide important ecosystem services, including carbon sequestration, water reservoir and habitat for both widespread and endemic organisms. When compared with boreal peatlands, our knowledge of the functioning of SSAP is poor, and it is necessary to raise awareness about their scientific and ecological value and to ensure their conservation. This article examines a broad base of historical and contemporary published research literature on the peatlands of Chile and Argentina, from 1843 onwards, to identify gaps in knowledge, implications for the assessment of peatland functioning, and targets for peatland conservation and management. To achieve this goal, we reviewed a total of 196 research papers/reports from across the peer-reviewed and grey literature. We conclude that gaps in our knowledge and understanding of SSAP have deeply undermined the development of effective conservation strategies for these understudied ecosystems. To reverse this situation, we recommend that future research and management efforts should aim: (1) to build an inventory of the peatlands that exist in SSAP, including their location and area; (2) to ensure land use planning prioritises the maintenance of SSAP ecosystem services; (3) to improve existing legislation and protocols of good and sustainable practice for extractive activities; and (4) to carry out an extensive awareness campaign aimed at the local population and key decision makers.