Here, we used physiological coupled with transcriptomic and proteomic analyses to investigate responses of the coral P. pukoensis to varied CO2 and alkalinity conditions. Focus was placed on the genes that showed the same trend of responses to the experimental condition manipulations. These conditions included normal CO2 (control), HC simulating high CO2 level expected in the year 2100 under the SSP5-8.5 scenario according to the IPCC36, HA simulating alkalinity enrichment into current seawater, and HCHA treatments simulating alkalinity enrichment into future acidified seawater