Even though Darwin's "On the Origin of Species" implied selection being the main driver of species formation, the role of natural selection in speciation remains poorly understood. In particular, it remains unclear how selection at a few genes can lead to genome-wide divergence and the formation of distinct species. We used a particularly attractive clear-cut case of recent plant ecological speciation to investigate the demography and genomic bases of species formation driven by adaptation to contrasting conditions. High altitude Senecio aethnensis and low altitude Senecio chrysanthemifolius live at the extremes of a mountain slope on Mt. Etna, Sicily and form a hybrid zone at intermediate altitudes, but remain morphologically distinct. Genetic differentiation of these species was analysed at the DNA polymorphism and gene expression levels by high-throughput sequencing of transcriptomes from multiple individuals. Out of ca. 18,000 genes analysed, only a small number (90) displayed differential expression between the two species. These genes showed significantly elevated species differentiation (FST and Dxy), consistent with diversifying selection acting on these genes. Genome-wide genetic differentiation of the species is surprisingly low (FST = 0.19), while ca. 200 genes showed significantly higher (FDR < 1%; mean outlier FST > 0.6) interspecific differentiation and evidence for local adaptation. Diversifying selection at only a handful of loci may be enough for the formation and maintenance of taxonomically well-defined species, despite on-going gene flow. This provides an explanation of why many closely-related species (in plants in particular) remain phenotypically and ecologically distinct despite on-going hybridisation, a question that has long puzzled naturalists and geneticists alike.