Low temperatures are one of the critical conditions affecting the performance and distribution of plants. Exposure to cooling results in the reprogramming of gene expression, which in turn would be mediated by epigenetic regulation. Antarctica is known as one of the most severe ecosystems, but several climate models predict an increase in average temperature, which may positively impact the development of Antarctic plants; however, under warmer temperatures, plants' vulnerability to damages from low-temperature events increases. Here, we evaluated the impact of these events on the acclimation process, with a focus on how methylation influences the induction of cold response genes. According to the results, an increase in the number of methylations in the promoter regions is associated with lower expression of these genes. Similarly, in populations where this relationship is observed, individuals acclimated to the projected climate change condition are more vulnerable, as their average temperature is lower in the face of a cold event compared to individuals acclimated to the current antarctic condition. This research is the first report highlighting the role of methylation in response to cold and its influence on the transcriptional responses of the antarctic plant Colobanthus quitensis facing climate change projections.