The role of biodiversity in natural forests is critical as a regulator of ecosystem function, productivity, and provision of ecosystem services. The objective was to analyse the conservation value of Nothofagus forests in Southern Patagonia (Santa Cruz and Tierra del Fuego provinces), Argentina, through integration of maps of potential biodiversity (MPB) and human footprint (HFM), which can help to improve the natural reserve designs through the spatial prioritization of their conservation values. To achieve the, first we determine that the different forest types presented different species assemblage with specific ecological niche requirements which justify differential conservation or management strategies. We used understory plants as proxy, and we selected indicator species of the understory plants for the following analyses. With these species we produce the MPB, and we found that the occurrence of MPB differ from the pattern of HFM according to the different forest types. After that, we identify woodland patches with special values of MPB and low HFM according to the different forest types, and analyzed if the distribution of MPB of the different forest types changed across the current natural protected reserve network, private and public lands. Finally, with these outputs, we propose new methodologies to enhance the current natural reserve network effectiveness. These outputs can be used as a tool to determine new strategies for management and conservation at landscape level in Southern Patagonia.