Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms potentially underpinning these processes. We used Tag-based RNA-seq to investigate the functional genomic consequences of long-term exposure to elevated pCO2 in Acropora millepora coral hosts and their in hospite Symbiodinium from natural CO2-seep environments in Milne Bay Province, Papua New Guinea. These files are the raw FASTQ read data for corals from Dobu and Upa-Upasina reef control and seep sites.