International efforts to protect biodiversity date back to the 1970s. The effectiveness of Multilateral Environmental Agreements and regional legal instruments has been influenced by national implementation. In this process, subnational governance plays a crucial role. Although policy implementation has been extensively investigated, its subnational dimension has been somewhat neglected, particularly in peripheral areas such as the Outermost Regions of Europe. These remote territories are critical areas in the global fight against biodiversity loss since their ecosystems’ richness makes them biodiversity hotspots. The article applies the knowledge cumulated in policy research to the implementation of biodiversity policy in two of these territories – Reunion Island (France) and the Canary Islands (Spain) – and analyzes policy implementation in the context of multi-level governance. The article questions whether and to what extent decentralization benefits biodiversity policies and highlights salient trade-offs: local empowerment versus fragmentation of competences; responsiveness versus subnational discretion; and accountability versus policy capture.