Identifying, surveying, monitoring and protecting natural forests is a major task in conservation biology. However, it is often challenging to identify which forest is natural, especially in human-altered regions such as the Mediterranean. Consequently, the distributions of natural Mediterranean forest types and their underlying factors are often unclear. Here, we attempt to explain the restricted and scattered distribution of naturalPinus pinea(Stone pine) forests in western Anatolia (Turkey) by comparing it with the distribution and ecology of the widespreadPinus brutia(Turkish pine) forests in this area. We used climatic and topographic predictors to test for differences between forests dominated by these two pine species. We modelled the realized niches of both pine species using the most relevant climatic predictors. Then, we compared soil data collected in the field, partly complemented with those published in the literature. We found small differences in climatic (precipitation and temperature) and topographic characteristics between the two forest types, which did not adequately explain the differences in the distribution range ofP. brutiaandP. pineadominated forests. Our data suggest that these two forest types mainly differ in soil characteristics. The primary habitat of naturalP. pineaforests is characterized by a low soil pH and calcium content. The rare occurrence of such soil conditions in western Anatolia likely shapes the scattered distribution ofP. pineaforests. Our study suggests that naturalP. pineaforests are rare habitats that should be in the focus of nature conservation.