Random amplified polymorphic DNA (RAPD) patterns show weak genetic differentiation between low- and high-elevation types of Scots pine (Pinus sylvestris L.) in dry continental valleys in the Alps. Two types of Scots pine (Pinus sylvestris L.), found either in the lowland or in the subalpine zone, are morphologically distinguished in the central-Alpine Valais (Switzerland), a dry continental valley. The low-elevation pine forests show signs of die-back since the early 1990s. We selected four elevational population pairs in the area, and two additional pairs in two other central-Alpine regions. Genetic differentiation between the two pine types, i.e. between elevations, and between two classes of vitality were studied using random amplified polymorphic DNA (RAPD). Growth in diameter and sapwood proportion was further assessed. Population pairs, with one exception, showed weak, but significant genetic differentiation (Φ_ST = 4.2% – 5.8%). On the other hand, there was no correlation between genetic data and the die-back observed. We consider disruptive evolution, postglacial migration, phenological separation or wind directions as possible explanations. Differences in growth and sapwood proportions supported the assumption of adaptation to local hydrological regimes.