Events below the freezing point increase with altitude. Freezing has been suggested as the first environmental filter that species have to pass to inhabit high altitudes. So far, few studies have conducted a common garden experiment of freezing resistance in high- and lowland plants; therefore it is still unclear what physiological and molecular mechanisms are involved in the differentiation between high- and lowland plants. Here, we studied freezing resistance and gene expressions in high- and lowland ecotypes of Arabidopsis halleri ssp. gemmifera. Seeds were collected from two altitudinal gradients, Mts. Ibuki and Fujiwara, and plants were grown in 22℃ and then moved to 4℃. We examined (i) whether the highland ecotype has genetically higher freezing resistance than the lowland ecotype and (ii) how they differ in gene expression during cold acclimation. The lowland ecotype from Mt. Ibuki had a lower freezing avoidance than the highland ecotype before cold acclimation, but similar on after cold acclimation. This was consistent with the expression pattern of cold-related genes in transcriptome analysis. However, the difference between the ecotypes was not observed on Mt. Fujiwra. These results suggest that adaptation to freezing is not necessarily consistent between altitudinal differentiations.