Identifying and characterizing the genetic basis of adaptation is one of the greatest challenges in evolutionary biology. Here, we combined a genome-wide analysis of patterns of molecular evolution with a candidate-gene approach to evaluate the role of neutral and non-neutral evolution in the adaptive history of stress responsive genes in two congeneric plant species with distinct habitat preferences. In particular, we studied patterns of molecular evolution in genes involved in irradiation and temperature stress responses in Cardamine resedifolia, a species found at high altitudes, and C. impatiens, which is found at low altitudes. In a first approach, the analysis of 3,000 putative orthologues, including genes involved in cold response, photosynthesis or in general stress responses, revealed that levels of selective pressure were heterogeneous between functional classes and between species, with cold responsive genes evolving particularly fast in C. resedifolia, but not in C. impatiens. The subsequent analysis of intraspecific genetic diversity in ten candidate genes, coupled with population structure inference, revealed no signatures for local adaptation across North-eastern Alps for both species. This suggests that adaptation and neutral processes have impacted the evolutionary history of the two species at different temporal scales (species vs. population)