Genetic variation along environmental gradients such as altitude provides understanding to genetic basis of adaptive evolution. Arabidopsis kamchatica subsp. kamchatica, a wild relative of A. thaliana, occurs from 30 m to 3000m asl in and around the Japanese Alps within a limited latitudinal range. In this study, we took advantage of the wide altitudinal distribution of A. kamchatica to detect the genetic basis of local adaptation. We pooled the DNA of 20 individuals in each of 19 populations. Six genes associated with flowering and hervivory-defence (GI, HEN2, DFL2, GL1, MAM1, TTG1) were chosen as candidate ecologically relevant genes. We sequenced a part of each of six genes amplified from the 19 pooled population samples using 454 pyrosequencing. Among 136 polymorphisms found, F_ST outlier test detected a SNP in GL1, a hervivory-defence gene associated with trichome variation, as a locus of ecological relevance. The SNP in GL1 showed significantly higher between-population genetic differentiation diverging from neutral expectations. Allele frequencies of the SNP in each population were correlated with trichome phenotypes and altitudes of the populations. The results suggest that GL1 is under diversifying selection and is associated with altitudinal adaptation.