Two colonies of Acropora millepora were acquired from Little Pioneer Bay and Northeast Orpheus near Orpheus Island research station. DNA and RNA were isolated from the same slurries of axial polyps (tips) and raidal polyps (sides). Tips included only the axial polyps. Methylomes were assayed with WGBS, MBD-seq, and methylRAD. Transcriptomes were assays with tag-seq.