The Atlantic Forest harbors one of the planet’s greatest biodiversities, characterized by a high degree of plant endemism. However, historical and contemporary processes of land use and occupation have resulted in the loss of about 75% of its original cover. Despite this, human populations have inhabited the biome for millennia, using a wide variety of native plants for medicinal purposes. This chapter aims to discuss how the use of native medicinal species can serve as a tool for conserving genetic diversity, biodiversity, and the traditional knowledge associated with them. Three case studies are presented: Varronia curassavica, Ilex paraguariensis, and Drimys brasiliensis. For each species, aspects related to medicinal use, ecology, geographic distribution, raw material acquisition, and genetic diversity are addressed. The integrated analysis of these studies shows that managing these species can simultaneously contribute to maintaining genetic variability and generating income for extractivist communities. Furthermore, the potential of medicinal plants in the Atlantic Forest goes beyond economic and therapeutic aspects, as their use is embedded in traditional landscape management systems that promote the conservation of forest cover, plant diversity, and ecological interactions. The expansion and strengthening of these systems depend on integrated actions and scientific support, which are essential for characterizing management practices and valuing the traditional knowledge associated with the conservation of the Atlantic Forest’s biological diversity.