Chocó is a region with high biodiversity and impacted by gold and platinum mining. This study determined the potential vulnerability of forests of Chocó to the loss of plant species in a context of mining activity. Field trips to different mining municipalities of the Chocó region were conducted in order to document the techniques of mineral extraction and the miners' perception on the performance and the environmental impact of mining in their territories. From data on gold and platinum production (1990-2012), the number of mining titles (2012-2013), number of mines and type of machinery used (2008-2012), the indices of mining activity (IAMAR) and relative mining production (IPMAR) were determined for all the territorial entities of Chocó. Additionally, the number of endemic species and threatened species was estimated and used to calculate the potential floristic vulnerability index (IVFP) regarding loss of species. The IVFP varied significantly between municipalities and subregions of the Chocó territory. The Municipalities with more IVFP were Condoto (9.43%), Istmina (7.75 %), Nóvita (7.74 %), Quibdó (7.64 %) and San José del Palmar (6.56 %). At the subregional level, San Juan (54.8%) had the highest IVFP. Mining in Chocó threats strategic ecosystems of global importance for the conservation of biodiversity and highlights the need for measures to prevent and mitigate the loss of species in areas with high vulnerability due to mining.