The need for a global priority list for threatened plants has been widely recognized by the conservation community, yet the threatened status of the majority of the world's plants species remains poorly known. This is especially true in the tropics and the oceanic islands of the Pacific, where progress towards the targets of the Global Strategy for Plant Conservation (GSPC) 2011-2020 is hindered by the paucity of complete species distribution data. Here we outline a new methodology to undertake threatened species assessments where detailed contemporary population data is lacking. This new interdisciplinary methodology draws upon the synthesis of archaeological and botanical data to calculate a percentage of long-term decline in habitat quality. We use this method to assess the threatened status of the endemic flora of Palau, Micronesia, a Pacific island nation known for its high levels of plant diversity and endemism, by utilizing data extending back to human colonization of the archipelago. For Palau, we calculate the percentage of a long-term decline in habitat quality to be 31-39% of the total available range of 55% of the endemic plant species. These data are also used to address a long debated question in the western Pacific: Are the origins of the savanna vegetation anthropogenic? Strong evidence for anthropogenic savannas in Micronesia support the estimated extent of historic deforestation in Palau. This new method worked well in our case study, and can be used in other locations with incomplete species distribution data to establish a first basis for conservation prioritization.