Anthropogenic CO2 is a major driver of current environmental change in most ecosystems1, and the related ocean acidification (OA) is threatening marine biota2. With increasing pCO2, calcification rates of several species decrease3, although cases of up-regulation are observed4. Here, we show that biological control over mineralization relates to species abundance along a natural pH gradient. As pCO2 increased, the mineralogy of a scleractinian coral (Balanophyllia europaea) and a mollusc (Vermetus triqueter) did not change. In contrast, two calcifying algae (Padina pavonica and Acetabularia acetabulum) reduced and changed mineralization with increasing pCO2, from aragonite to the less soluble calcium sulphates and whewellite, respectively. As pCO2 increased, the coral and mollusc abundance was severely reduced, with both species disappearing at pH < 7.8. Conversely, the two calcifying and a non-calcifying algae (Lobophora variegata) showed less severe or no reductions with increasing pCO2, and were all found at the lowest pH site. The mineralization response to decreasing pH suggests a link with the degree of control over the biomineralization process by the organism, as only species with lower control managed to thrive in the lowest pH.