ABSTRACT Understanding the factors that affect native plant communities is essential to protect floristic diversity, particularly in Mediterranean agroecosystems. The Chilean Mediterranean-climate area supports high species richness and levels of endemism, and harbors the main fruit production. We investigated whether the richness of native and non-native flora differs between two Mediterranean climate areas of Chile with contrasting rainfall levels in both cultivated and uncultivated habitats. Thirteen fruit farms under conventional management were prospected in the spring of 2015 and of 2016 by sampling in square meter quadrants (N = 3,630). A total of 191 vascular plants were found, 48.2 % of them native, 50.3 % non-native and 1.6 % not identified. Species richness was low in both areas and habitat types. However, there were more native species in uncultivated habitats in the Mediterranean-to-desert transition area than in the mesic Mediterranean area, and the contrary was observed for non-native species. Our results suggest that wetter Mediterranean climate areas are more prone to the establishment of non-native plant species.