Elevation gradients generate different environmental conditions. This environmental differentiation can influence morphological adaptation, habitat isolation, reproductive isolation, and pollinator limitation in plants. Habitat differentiation and isolation often act first on phenotypic traits and then on genotype variation, causing genetic divergences between populations. We evaluated the effect of elevation on morphological traits, reproductive isolation, and pollinator limitation in Croton aff. wagneri in dry shrublands of inter-Andean valleys in Ecuador. We measured morphological traits of Croton at three elevations and carried out experimental pollination crosses between and within each population at different elevations to assess the degree of reproductive isolation and pollinator limitation. Morphological traits such as leaf thickness, plant volume, inflorescence length and inflorescence number were dissimilar between plants in different elevations. There was evidence of incipient reproductive isolation between plants in populations at the highest and the lowest studied elevations. Pollination experiments within each elevation showed a limitation of pollinators in Croton in the highest elevation. Intrinsic barriers to pollen dispersal and ecological divergence can produce reproductive incompatibilities between individuals with different traits along the Croton elevation gradient.