The function of DNA methylation in shellfish where the limited amount of DNA methylation is predominantly found in gene bodies is not completely understood. One explanation is that the role of gene body DNA methylation is dependent on gene function, a potential phenomenon that has arisen from selective pressure on lineage-specific life history traits. We know that in other taxa epigenetic marks are associated with phenotypes independent of genetic variation, the environment can influence DNA methylation, and epigenetic marks can be inherited. While we have examined DNA methylation in bivalves for almost a decade, there is still not convincing evidence that the function(s) align with some of the early hypotheses. It has also been suggested that DNA methylation might not have a biological function. DNA methylation landscapes will be described in bivalves and specific data sets will be presented including looking at the role of DNA methylation in genomic regulatory function and heredity in oysters. In addition, perspectives will be provided on how to address the function of epigenetic mechanisms in mollusks.