The brazilwood tree Paubrasilia echinata is endemic to the Atlantic Forest of Brazil and is categorized as Endangered on the IUCN Red List as a result of habitat loss and overexploitation. Phylogenomic analysis has identified five groups based on genotype, including the arruda-RJ lineage endemic to the state of Rio de Janeiro. We propose a prioritization classification protocol for Atlantic Forest fragments and evaluate the effectiveness of conservation for this species in Rio de Janeiro. We collated a total of 164 occurrence records of P. echinata from fieldwork during 2004–2024 and from the Global Biodiversity Information Facility. We classified forest fragments containing the species as high, medium or low priority for conservation. The arruda-RJ lineage persists in 43 forest fragments in the coastal region, 30 of which are documented for the first time here. Most forest fragments are small and have an uneven population structure. Urbanization is the primary threat to the survival of this lineage. We documented protected areas in 33 fragments, and identified conservation opportunities. The greatest number of forest fragments is in the northern region where there are the most protected areas and the brazilwood populations hold the greatest local genetic diversity. We propose targeted conservation actions for P. echinata arruda-RJ in eight forest fragments identified as high priority and with the greatest potential for conservation of the lineage. We identified 25 fragments as medium priority and 10 fragments as low priority. Our approach is applicable to other lineages of P. echinata and is aligned with Global Biodiversity Framework targets.
