Endemism in mountain ranges is considered to be the result of a number of factors, including restriction to refugia during Pleistocene climate fluctuations. However, isolation in glacial refugia cannot explain the origin of narrowly endemic taxa restricted to formerly heavily glaciated areas. Here, we investigate the phylogeny of two narrowly endemic species, Euphrasia inopinata and E. sinuata (Orobanchaceae), found exclusively in formerly heavily glaciated areas of the eastern European Alps. As both species are diploid and very similar to the widespread (allo)polyploid E. minima, we test whether the restricted distributions of E. inopinata and E. sinuata are relictual, i.e., the two species are ancestral diploid remnants of a polyploid complex, or whether they are derived, i.e., the two species are peripheral segregates of a more widespread diploid. Based on ITS sequence and AFLP fingerprint data it is shown that E. inopinata and E. sinuata, whose diploid ploidy level is confirmed for all analysed individuals via flow cytometry, are phylogenetically closely related to diploid E. alpina s. l. (series Alpinae) instead of E. minima (series Parviflorae). In addition, there is no evidence that these two diploid species participated in the formation of allotetraploid E. minima. Thus, E. inopinata and E. sinuata are interpreted as peripheral segregates of the widespread E. alpina s. l.. Shifts in pollination system from allogamy in E. alpina s. l. to autogamy in E. inopinata and E. sinuata, genetic drift in small populations, and geographic isolation at the periphery of the range of E. alpina s. str. probably contributed to the morphological and ecological differentiation of E. inopinata and E. sinuata.