Ocean acidification can affect various physiological and behavioural traits in fishes. However, some fish species seem to benefit, exhibiting increased population densities at natural CO₂ seeps. To investigate the molecular mechanisms underlying this advantage with ocean acidification, we sequenced the brain transcriptomes of four fish species from temperate natural CO₂ seeps and nearby control sites in White Island, New Zealand. Common triplefin Forsterygion lapillum and crested blenny Parablennius laticlavius, which have double the density at vents with adaptive potential to ocean acidification, displayed 429 and 108 differentially expressed genes (DEGs), of which both include core circadian rhythm genes. Previous studies reported environmental changes can reset circadian rhythm in vertebrates by changing expression of core circadian rhythm genes, which can adjust the downstream gene expression for an acclimation. However, Yaldwin’s triplefin Notoclinops yaldwyni and blue-eyed triplefin Notoclinops segmentatus, which experienced a decline in density at the seeps, revealed 143 and 31 DEGs. And the Yaldwin’s triplefin also indicated significant expression changes to core circadian rhythm genes. Our study suggests that future ocean acidification might cause changes to key functions, such as the circadian change, universal across many species and ecosystems necessary for dealing with future ocean acidification, however, these changes may not always be adaptive in wild populations.