Amplified Fragment Length Polymorphism (AFLP) was used to clarify the glacial history of the rare, disjunctly distributed, alpine cushion plant Androsace wulfeniana, which is endemic to the Eastern Alps (Austria and Italy). Disjunct populations in the Dolomites are genetically very distinct from those in the main distributional area. It is hypothesized that they are descendants of long-term isolated glacial survivors and are not a result of recent long-distance dispersal. Within the main distributional area of the species in the central Eastern Alps, two groups of populations can be distinguished, which are congruent with hotspots of rare relictual vascular plant taxa. In the taxonomically closely related A. brevis growing in the Southern Alps (Italy, Switzerland), no genetic-geographical structure was found. Genetic variation is extremely low in disjunct populations of A. wulfeniana in the Dolomites and in A. brevis. In contrast, in the main distributional area of A. wulfeniana, genetic variation is similar to that of the colonizing widespread congener A. alpina. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 141, 437–446.