(1) The evolution of species or ecotypes can occur gradually through neutral and adaptive genetic changes. To explore the influence of natural selection during early phases of divergence, morphological and ecological discontinuity and its adaptive significance were investigated in six pairs of alpine and independently evolved montane populations of Heliosperma pusillum .; the latter are usually taxonomically recognised at the species rank in spite of their highly doubtful debatable taxonomic value. (2) We tested whether environmental conditions – characterised by Landolt indicator values from vegetation surveys and temperature measurements – and morphology of alpine and montane populations differ discretely and in parallel across six population pairs. By reciprocal transplantation experiments in natural environments in two population pairs and in climate chambers for five population pairs we compared fitness of native vs. non-native individuals. (3) Alpine and montane populations differed in environmental conditions and morphology within each pair. Morphological differentiation occurred in parallel and correlated with environmental, but not with genetic distances. In both environments, native individuals had higher establishment success and plant size. (4) Differentiation of the independently evolved montane populations is driven by natural selection and parallel, independent adaptation in response to drought, lower irradiance and higher, less fluctuating temperatures in montane and alpine populations, respectively. Our study system exemplifies rapid, parallel evolution leading to morphologically and ecologically strongly divergent, though fully interfertile, ecotypes.