Environmental variation is widely viewed as a major force driving morphological change and speciation. Although many environmental attributes are potentially critical for adaptive responses within and between species, the individual and relative importance of these diverse attributes remain poorly understood. Here we combine a geographical information systems (GIS)-based analysis of environmental variation with a multipopulation analysis of phenotypic, physiological, and genetic variation, to generate and test hypotheses of environmental factors likely driving adaptive divergence within and between two wild Andean plant species. First, we document large environmental differences between population locations of the two species, and among regions within species. Second, we show evidence for inter- and intraspecific differences in genetically based phenotypic and physiological variation. Third, combining these data, we report evidence for trait–environment associations both among populations within species, and between species, that are strongly indicative of recent and rapid adaptive responses. Finally, we show that these trait–environment associations cannot be simply explained by genetic relatedness within species, reinforcing our inference that local, regional, and species-wide environmental conditions are responsible for phenotypic and physiological diversification. The strongest trait–environment associations involve temperature and precipitation gradients, suggesting these climatic factors are predominant drivers of adaptive diversification in these species.