Genome-wide DNA methylation studies using bisulfite sequencing have been hampered by high costs and potential biases due to methods in non-model organisms. To improve understanding of differences in the bisulfite sequencing methods and ultimately how genome-wide DNA methylation studies are carried out, we compared three methods for quantifying DNA methylation at single base pair resolution: Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), and Methyl-CpG Binding Domain Bisulfite Sequencing (MBDBS). We used replicate individuals from two reef building coral species with contrasting environmental sensitivity, the more resistant Montipora capitata and the more sensitive Pocillopora acuta.