The afro-alpine region in Eastern Africa encompasses the elevated plateaus andrnmountains in Ethiopia and the isolated high mountain peaks in Kenya, Tanzania,rnand Uganda, often referred to as biological 'sky islands'. The age of the flora onrnthese mountains has been debated. Based on the high level of endemism, it hasrnbeen suggested that the flora is old and might represent Tertiary relicts. Othersrnhave argued that some plant groups are young and have colonized thesernmountains during the Pleistocene. The impact of the glacial-interglacialrnoscillations of the Pleistocene on the origin and geographical structuring of therngenetic diversity in many temperate plant species has been well documented,rnwhereas only few studies for the afro-alpine plant speices have so far beenrnconducted. Here we use a combination of molecular dating and phylogeographicrnanalysis of selected plant species to provide insight into the evolution of plantsrnin the afro-alpine region. A fossil calibrated multilocus species tree based onrntwo nuclear and three plastid DNA regions was used to estimate the age of thernafro-montane endemic Lychnis (Caryophyllaceae). Furthermore, AmplifiedrnFragment Length Polymorphism (AFLP) fingerprinting was used to assess therngenetic diversity and population genetic structure of seven plant species: twornheather species from the ericaceous zone, Erica arborea, E. trimera (Ericaceae),rnand five species from the afro-alpine zone proper: Carex monostachya, C.rnrunssoroensis (Cyperaceae), Lysimachia serpens (Primulaceae), Dicrocephalarnchrysanthemifolia and Haplocarpha rueppellii (Asteraceae). The multilocusrnspecies tree analysis have placed the mean age of the afro-montane Lychnis torn2.28-5.8 Myr (million years) corresponding to late Miocene to the late Pliocenernand thus indicating a Tertiary relicts. The results from the AFLP analysisrnshowed that all investigated species have very low levels of overall generndiversity, suggesting bottlenecks in small refugial populations duringrnunfavourable climatic periods. The populations of E. trimera and H. rueppelliirnshowed relatively distinct geographical structuring of the genetic variation,rnsuggesting long-term isolation of the former in at least three separate places andrnof the latter in two refugial populations. The lack of common phylogeographicrnpatterns indicates that different species have responded individually to thernPleistocene climatic oscillations.rnKey words: AFLP, Afro-alpine, Afro-montane, Lychnis, Erica arborea, Ericarntrimera, Carex monostachya, Carex runssoroensis, Lysimachia serpens,rnDicrocephala chrysanthemifolia, Haplocarpha rueppellii, Molecular dating,rnPhylogeography, Plio-Pleistocene, Tertiary-relicts.