Landscape genomics offers powerful tools to assess the influence of habitat loss on genetic diversity and functional connectivity, and to identify adaptations to local environmental conditions. At Instituto Tecnológico Vale, located in the mouth of the Amazon River, we employ these tools to generate the knowledge needed to help mitigate the negative effects of mining on Amazon biodiversity. Specifically, we developed an analytical pipeline to analyze next-generation sequencing data and study how habitat loss led by mining impacts genetic diversity and gene flow in threatened endemic plants from Amazonian Savannas. Relying on different environmental association approaches we are also in the process of identifying adaptations to local environmental conditions that could optimize restoration programs.