Plant species richness and endemism on oceanic islands is dependent on island age, size, elevation and distance to nearest source of migrants. Mainland ‘island’ systems, such as the cool-adapted tropical-alpine flora of the mountains in Africa, are less well studied. Here we analyse the tropical Afroalpine flora, found on highly isolated mountains straddling the equator. Using the β-sim index in a hierarchical clustering approach combined with ordination methods and mantel tests, we locate four geographical groups: West Africa, northern East Africa, western East Africa and eastern East Africa. We show that these groupings are better explained as the consequence of geographical isolation rather than environmental filtering. We further show that the species richness of the tropical Afroalpine mountain regions—similar to oceanic islands—can be explained by a model including age, area size, elevation and isolation. Levels of endemism are best explained by species richness in combination with area and isolation. Overall we develop a comprehensive model of the species richness, endemism and composition of the tropical Afroalpine flora.