<p dir="ltr">In the European Alps, plant species have persisted through major geological and climatic changes, leaving genetic patterns of divergence. While such patterns are often linked to Pleistocene glacial refugia and ecological factors, they may also trace back to pre-glacial events.</p><p dir="ltr">We combined RAD-seq phylogenomic data, demographic modeling, and ecological analyses to determine whether genetic variation in ten alpine willows (<i>Salix</i> spp.) reflects pre-glacial divergence or glacial dynamics, and to assess the role of extant environmental differentiation.</p>