The role of epigenetic regulation should be evaluated in the context of natural environments, as each organism inhabits a specific set of environments in natural systems. We conducted a series of molecular phenology studies in a natural population of Arabidopsis helleri to understand plant adaptation to seasonal environments using RNA-seq and ChIP-seq. Seasonal changes of H3K27me3 were found to be prominent compared to diel changes and were expected to play a critical role in seasonal adaptation. Furthermore, delayed seasonal changes of H3K27me3 from those of H3K4me3 were observed in some genes, and in these genes, H3K27me3 behaved as a mechanism to track past transcriptional activities. Among them, AhgFLC, a homolog of the key flowering repressor in the vernalization pathway, was characterized by the largest delay of H3K27me3 from H3K4me3. Two-year high-frequency ChIP-qPCR analyses identified the unidirectional changes of H3K27me3 between the TSS and the gene body regions of AhgFLC. This unidirectional change of H3K27me3 serves as a mechanism for unidirectional transitions of plant life stages in a seasonal environment. In conclusion, one of the major roles of H3K27me3 is the robust control of seasonal gene expression under fluctuating natural conditions. Because the level of H3K27me3 accumulation depended on the length of cold periods, we expected that the seasonal dynamics of histone modifications may be disrupted by global warming.