This study presents a 40,000-year-old pollen record from Los Tollos Lake in the Baetic-Rifan region of southernmost Spain. The data offer insights into the past ecosystems of a current biodiversity hotspot situated at the ecotone between the Atlantic and the Mediterranean. This new sequence encompasses Mediterranean and Ibero-North African sclerophylls, broad-leaf trees, conifers, and Tertiary relicts. The full-glacial abundance of mesothermophytes, particularly oaks, is among the highest recorded for the European Quaternary. Notably, the presence of ecologically significant pollen taxa, which are poorly dispersed and currently occur outside the study area, suggests that this biodiversity hotspot was more extensive in the Pleistocene. During the period of c. 40.8–36.5 ka, three Artemisia maxima at 40.6, 38.9, and 36.9 ka coincide with decreases in Quercus, indicating the spread of steppes in response to the abrupt coolings of the GS10, GS9 (HS4), and GS8 events. Similarly, increases in Quercus around 41, 40, and 37.2–38.3 ka parallel the GI10, GI9, and GI8 warm events. A forested period from 36.5–32 ka includes oak expansions during the GI7 and GI6 interstadials. From 32 to 19.2 ka, more xerophytic vegetation is observed, including the HS3, GS5-GS3, HS2, and GS2.1b-c cold spells, although the correlation with vegetation changes is not synchronous. As early as approximately 21 ka, Artemisia definitively declines, while the region was reforesting, likely due to the presence of stationary populations of broadleaf trees and conifers in the southern Baetic mountains. From approximately 12 ka onwards, the highest values of angiosperm trees are recorded, with oaks dominating throughout most of the Holocene. The pollen record and the correlation with marine records suggest a more intense hydrological regime during the first half of the Holocene, but there is also archaeobotanical evidence for human activity during the second half, resulting in a more open landscape, making it difficult to discriminate the impact of each factor. Some abrupt aridity events during the Holocene coincide with small variations in tree cover, particularly at 9.2, 8.2, 6.8, 5.5–4.8, 4.2, and 2.8 ka. Since the Neolithic and during the metallurgic stages, forest species, especially broad-leaf trees, experienced range retraction accompanied by population extinctions. The region's plant communities have been subject to fire regimes since the Pleistocene, seemingly dependent on the available tree biomass.