Although UV radiation is more stressful at higher elevations, highland species may have altered their UV tolerance evolutionarily. We employed Arabidopsis ecotypes to evaluate the generality of UV damage on DNA and growth along elevation. We cultivated four ecotypes of A. thaliana (Dzi and Sha from highland, and Tsu-1 and Col-0 from lowland) and three ecotypes of A. halleri subsp. gemmifera (populations from 300, 760 and 1300 m in Mt. Ibuki) with or without supplementary UV-B. We harvested plants three times and determined biomass, the relative growth rate (RGR), and the level of cyclobutane pyrimidine dimer (CPD) as UV damage. At early stage, lowland ecotypes were more sensitive to enhanced UV-B than highland ecotypes, as accumulating higher CPD level and greater inhibition in biomass production. At later stage, the CPD level and growth inhibition became similar or even smaller in lowland ecotypes. These results suggest that the response to UV stress was more constitutive in highland ecotypes, whereas more inducible in lowland ecotypes. These ecotypic differentiations were common in the two Arabidopsis species, suggesting that local adaptation occurred in parallel.