Here, temporal changes in genome-wide patterns of DNA methylation in the staghorn coral Acropora cervicornis in the island of Culebra, PR were explored for a 17-month period. A total of 162 polymorphic loci were identified using Methylation-Sensitive Amplified Polymorphism (MSAP). Among them, 83 of these fragments displayed changes in DNA methylation changes that were significantly correlated to seasonal variation as determined mostly by changes in sea water temperature. Remarkably, the observed time-dependent change in DNA methylation patterns is consistent across coral genets, coral source sites and site-specific conditions studied. Overall, these results are consistent with a conserved epigenetic response to seasonal environmental variation. These findings highlight the importance of including seasonal variability into experimental designs investigating the role of epigenetic mechanisms such as DNA methylation in responses to stress.