Understanding speciation on oceanic islands is a major topic in current research on island biogeography. Within this context, it is not an easy task to differentiate between the influence of elevation as an indicator for habitat diversity and island age as an indicator for the time available for diversification. One reason for this is that erosion processes reduce the elevation of islands over time. In addition, the geographic distance to source ecosystems might differ among habitats, which could lead to habitat-specific reduction of species immigration, niche occupation and diversification. We used the percentage of single island endemic species (pSIE) in five different zonal ecosystems (distributed in altitude) on the Canary Islands as an indicator for diversification. We tested whether diversification increases with altitude due to a greater ecological isolation of high elevation ecosystems on oceanic islands under the assumption of a low elevation source region on the mainland. In addition we tested whether the ‘hump-shaped’ (unimodal) relationship between pSIE and island age as well as the linear relationship between species richness and pSIE is consistent across spatial scales. We also analyse a potential influence of island area and habitat area. We found that pSIE increases with elevation. The relations between species richness as well as age with pSIE are consistent across scales. We conclude that high elevation ecosystems are ecologically isolated. Surprisingly, the altitudinal belt with the strongest human influences has the highest values of pSIE. We successfully transfer the ‘general dynamic theory of island biogeography’ to the ecosystem scale, which provides multiple opportunities for future studies. With this approach we find that the effects of elevation on diversification can be separated from those of island age.