The afro-alpine region s.l. refers to the high mountains of Ethiopian and Topical East Africa.rnThe flora of this region is unique in composition compared to the surrounding lowlands andrnsubdivided into three altitudinal vegetation belts: the afro-montane, ericaceous and afro-alpinernbelts. The origin and extant distribution of the flora had been influenced strongly by thernPleistocene climatic oscillations. During glacial (cold) periods, the afro-alpine and ericaceousrnbelts were broad while the afro-montane belt was reduced and fragmented. The montanernforests had probably persisted in refugia located at mountain foothills or in river basins. Afromontanernforest was extensive during interglacial (warm) periods whereas the afro-alpine andrnericaceous belts were compact. Based on amplified fragment length polymorphisms (AFLPs)rndata, we provide insights into the origin, fragmentation and evolution of some key afromontanernspecies in relation to Pleistocene climatic oscillations. In view of this, we focus onrnthe genetic diversity and population genetic structure of these afro-montane plant taxa withoutrnobvious long distance dispersal morphology and that are widely distributed in the EastrnAfrican mountain systems (i.e., Erica arborea, Hypericum revolutum and Lobelia giberroa).rnRegardless of some general observed phylogeographic trends such as divergent lineages,rncontact zones, altitudinal shift and complex refugia, our analyses highlight that each speciesrnhad a unique phylogeographic pattern and the geographical consistency of the genetic patternsrndiffer considerably. Our observation further suggest that L. giberroa and H. revolutum geneticrngroups occupied geographically well defined areas while the geographic pattern of E.rnarboreia is rather complex. Furthermore, we have attempted to identify important areas forrnconservation of the current study species based on concepts of hotspots of intraspecificrndiversity and evolutionary significant units (ESU). This approach could be followed to assessrnor design appropriate genetic conservation priorities as well as a robust sampling strategiesfor further studies. This study is the first of its kind concerning the impacts of Pleistocenernglaciations on the genetic structures of afro-montane/-alpine plants and it will certainly guidernto scope future phylogeographic studies in Africa. In prospect, it is important to cover thernwhole distribution range of the study species to have more complete phylogeographic picturernof the region. In addition, it is appropriate to investigate many wide-spread plant species withrnwell-documented fossil data and use appropriate genetic criteria to deduce the impact ofrnPleistocene climatic fluctuations on the genetic structure of the present day afro-montane/-rnalpine flora.rnKey words: AFLP, Afro-alpine, Afro-montane, Conservation, Erica arborea, Hypericumrnrevolutum, Lobelia giberroa, Phylogeography