Organisms spanning numerous taxa have been shown to mediate stress responses by utilizing epigenetic mechanisms, notably DNA methylation. This study aimed to characterize the seasonal patterns in DNA methylation in the gill tissue of the flat tree oyster (Isognomon alatus) and its response to temperature, pH and salinity variations in Miami’s Northern Biscayne Bay. Flat tree oyster specimens attached to mangrove prop roots by their byssus were sampled from ten distinct sites across the bay that differed by their geographical and physicochemical characteristics. Quantification of DNA methylation from gill tissue show a sinusoidal-like seasonal pattern throughout time. Despite a clear seasonal trend, analyses revealed that there is no significant correlation between abiotic parameters (temperature, pH, salinity) and variations of DNA methylation. On the other hand, this report showed that methylation levels of oysters were highest at sites with the greatest potential sources of pollution. Further studies are required to determine if water pollutants or other chemical factors may be influencing seasonal patterns in DNA methylation and if observed seasonal trends are consistent throughout subsequent years.