1. The high diversification rates of plant lineages in the Mediterranean Basin hotspot have been linked to a complex interaction of climatic stressors, geographic isolation and soil type, but the question remains as to which of these factors has been the most significant environmental driver of recent speciation.

2. Here, we draw on distributional data for the entire endemic flora of the Iberian Peninsula, together with DNA-based phylogenies and spatial phylogenetic methods, to explore patterns of relative phylogenetic endemism at different spatial resolutions and phylogenetic scales (superclades) and assess how environmental factors contribute to explain these patterns.

3. We found that recent diversification of angiosperms as a whole, and particularly of eudicots, has been boosted by environmental stressors including high values of soil pH and dry-seasonal climatic conditions, while diversification of monocots has not been associated with soil conditions but with high elevation and less seasonal climate.

4. Synthesis. These results provide robust insights into the environmental factors driving recent plant diversification in the Mediterranean Basin, including a role of soil properties that had not been quantified before. The contrasting environmental drivers of diversification in Eudicots and Monocots highlight the importance of analyzing spatial phylogenetic patterns at multiple phylogenetic scales to get a better understanding of the processes that shape biodiversity.