• Although, for both marsupials and rodents, Protected Area alone are not enough to contribute to the conservation of species, when we include all protection categories, the level of contribution of protected areas increases. • Less than 20% of the potential distribution of species is within Protected Areas. • Rodents have only 9.56% of their habitat protected, while marsupials have even less coverage. • High species richness areas coincide with the “arc of deforestation,” a region of intense human impact. • Natural areas protected in Conservation Units (UC’s), together with Indigenous Territories (IT’s), constitute the most crucial defense mechanisms for biodiversity. Accelerated deforestation in the Brazilian Amazon threatens biodiversity, particularly small non-volant mammals such as marsupials and rodents. This study evaluates the role of Protected Areas (SPAs and SUAs) and Indigenous Lands (ILs) in conserving these species. Findings reveal that less than 20% of the species’ potential distribution lies within Protected Areas. Rodents have only 9.56% of their habitat protected, while marsupials have even less coverage. However, combining all protection categories (SPAs, SUAs, and ITs) significantly increases conservation effectiveness, covering up to 25% of species distributions. Areas of high species richness coincide with the “arc of deforestation,” a region experiencing intense human impact. Amazonian savannas, though hosting unique biodiversity, are underexplored and increasingly threatened by agricultural expansion. Key species such as Caluromysiops irrupta and Proechimys echinothrix rely heavily on these protected savanna habitats. The study emphasizes the urgent need to expand and strengthen protected areas, particularly in biodiversity-rich regions like the Amazonian savannas. Indigenous Lands are crucial not only for environmental preservation but also for maintaining cultural and traditional knowledge. Effective conservation requires robust public policies, ecological restoration projects, and collaboration with local communities, supported by advanced monitoring technologies to ensure long-term protection.