Phylogeographic studies in the high mountains of Africa are hampered by the limited material available, resulting in insufficient knowledge of taxonomic variation within and among closely related species. Here, we address genetic and morphological variation in three grass species, of which one (Deschampsia angusta) has been reported as narrowly endemic and vulnerable whereas Deschampsia cespitosa and Koeleria capensis are widely distributed also outside the afro-alpine region. We used amplified fragment length polymorphisms (AFLPs) to assess genetic structuring and diversity in material collected during recent field expeditions and included additional herbarium material in morphometric analyses. The plants identified as the endemic D. angusta were genetically very similar to those identified as D. cespitosa from the same mountain (Mt Ruwenzori), forming a single coherent genetic group in STRUCTURE analysis. The plants identified as D. angusta seem to represent extremes of continuous gradients of morphological variation within a single, variable species, D. cespitosa. We found that the afro-alpine material of Deschampsia consists of three genetically very distinct groups corresponding to the three mountains investigated, suggesting persistence in isolated afro-alpine refugia during one or more glacial cycles. In contrast, we found no clear genetic structure in K. capensis. This species harbored very little genetic diversity in all six mountain areas examined, and little genetic rarity except in the Ethiopian Simen Mts. This pattern may be explained by recent colonization of the afro-alpine region from a single source population or possibly by extensive recent gene flow combined with bottlenecks. We found, however, some differentiation between different K. capensis populations from Mt Kilimanjaro, corresponding to two described varieties. This study demonstrates the need for further taxonomic exploration of the enigmatic flora of the isolated afro-alpine ‘sky islands’ and highlights that different species may have conspicuously different phylogeographic histories.