The Galápagos Islands are globally renowned for their ecological value and as a world symbol of scientific discovery; however the native biodiversity of this unique region is currently under threat. One of the primary concerns is the detrimental impact of approximately 750 nonnative plants introduced over the last 500 years of human presence in the archipelago. In addition to these known introduced species, there are an additional 62 vascular plants classified as "doubtful natives," where native status remains unclear. To help address the questions of provenance regarding these doubtfully native species and their impact on highland ecosystems over the past 500-1000 years, we analyzed plant macrofossils in sedimentary records. Appropriate species classification (native or introduced) was determined using baseline data of species presence on the islands. We confirmed that six plants (Ageratum conyzoides, Solanum americanum, Ranunculus flagelliformis, Brickellia diffusa, Galium canescens, and Anthephora hermaphrodita) once considered doubtful natives or introduced are actually native to the Galápagos flora. These results have relevance not just for the Galápagos but also many other oceanic islands in demonstrating the application of palaeobotanical data to conserving and restoring native biodiversity.