Punta de Gavilanes (Mazarrón Bay, Spain) was occupied from third millennium cal BC to the first century BC. Overall, the archaeobotanical remains suggest that agriculture and gathering coexisted in the site since the beginning of the occupation of the site. Depending on the sea level variation, the site passed from island in the middle Holocene to peninsula in the late Holocene. Seeds from this archaeological site associated with radiocarbon dates of ≈ 4200 and ≈ 1500 cal years BP include specimens of eight species of shrubs and trees, of which a winter flowering shrub (Coronilla talaverae Lahora and Sánchez-Gómez), is an endangered species that no longer occurs on Punta de Gavilanes area. The seeds of this endemic Coronilla species are associated with materials dated ≈ 3900 cal years BP in a Bronze Age cultural context. The vanished species was presumably locally exterminated by human alteration of its natural habitat or because of environmental changes. The species of Coronilla identified from Punta de Gavilanes is known from relatively distant seashore areas. This endangered species could be effectively preserved by reintroduction to areas that it occupied prior to human alteration, in particular Punta de los Gavilanes.