Maytenus senegalensis subsp. europaea is a shrub belonging to the Celastraceae family, whose only European populations are distributed discontinuously along the south-eastern coast of the Iberian Peninsula, forming plant communities with great ecological value, unique in Europe. As it is an endangered species that makes up plant communities with great palaeoecological significance, the development of species distribution models is of major interest under different climatic scenarios, past, present and future, based on the fact that the climate could play a relevant role in the distribution of this species, as well as in the conformation of the communities in which it is integrated. Palaeoecological models were generated for the Maximum Interglacial, Last Maximum Glacial and Middle Holocene periods. The results obtained showed that the widest distribution of this species, and the maximum suitability of its habitat, occurred during the Last Glacial Maximum, when the temperatures of the peninsular southeast were not as contrasting as those of the rest of the European continent and were favored by higher rainfall. Under these conditions, large territories could act as shelters during the glacial period, a hypothesis reflected in the model’s results for this period, which exhibit a further expansion of M. europaea’s ecological niche. The future projection of models in around 2070, for four Representative Concentration Pathways according to the fifth report of the Intergovernmental Panel on Climate Change, showed that the most favorable areas for this species would be Campo de Dalías (southern portion of Almería province) as it presents the bioclimatic characteristics of greater adjustment to M. europaea’s ecological niche model. Currently, some of the largest specimens of the species survive in the agricultural landscapes in the southern Spain. These areas are almost totally destroyed and heavily altered by intensive agriculture greenhouses, also causing a severe fragmentation of the habitat, which implies a prospective extinction scenario in the near future.