The extent and pattern of DNA methylation on different genomic elements vary greatly across Metazoa; in particular, bilaterian vertebrates and invertebrates show striking differences regarding methylation on the gene bodies. It has been hypothesized that gene body methylation is the ancestral state for Metazoa; however, sampling outside of Bilateria is minimal. From this perspective, we survey 76 Cnidarian species spanning all major groups using computational methods to probe the extent of DNA methylation, and we show that methylation on the gene bodies is prevalent in Cnidaria, with a few instances of loss. We also show that gene body methylation correlates with sequence conservation and expression variability. Notably, several species show derived methylation status on orthologous genes. In addition, gene bodies are preferentially targeted over repetitive elements, and both gene body methylation and repeat methylation change with repeat content. Taken together with evidence from other Metazoan taxa, this work supports the hypothesis that methylation preferably targeting gene bodies, not regulatory sequences or repetitive elements, was the ancestral state for Metazoa.