In the California Current ecosystem, global climate change is predicted to trigger large-scale changes in ocean chemistry within this century. Ocean acidification – which occurs when increased levels of atmospheric CO2 dissolve into the ocean – is one of the biggest potential threats to marine life. We compared the effects of chronic exposure to low pH (elevated pCO2) on the behavior, physiology, and patterns of gene expression in two congeneric species of nearshore rockfish (genus Sebastes), integrating responses from the cellular to whole organism level. Our findings indicate that these congeners, despite inhabiting the same environment (kelp forests), have very different tolerances and sensitivities to future ocean conditions. Copper rockfish (S. caurinus) exhibited changes in brain function, reduced critical swimming speed, depressed aerobic scope, and increases in the expression of transcription factors and metabolic genes at high pCO2 exposure. Blue rockfish (S. mystinus), in contrast, showed no significant changes in neurobehavior, swimming physiology, or aerobic capacity, but did exhibit significant changes in the expression of muscle structural genes as a function of pCO2, indicating acclimatization potential. The capacity of long-lived, late to mature, commercially important fish to acclimatize and adapt to changing ocean chemistry over the next 50-100 years is likely dependent on species-specific traits and evolutionary history.