A quantitative compilation of carbonate skeletal mineralogy through the Phanerozoic shows a progressive replacement of low-Mg calcite by aragonite. This general trend overrides the subsidiary trend of greenhouse intervals favoring biogenic low-Mg calcite mineralogies (calcite seas), and icehouse intervals facilitating aragonite + high-Mg calcite mineralogies (aragonite seas). The replacement of low-Mg calcite by aragonite was, however, achieved episodically at mass extinction intervals. In particular, the end-Permian extinction both preferentially removed species bearing “unfavorable” low-Mg calcite, and allowed the selective radiation of biota with “favorable” aragonite. This demonstrates the importance of incumbency in the evolution of skeletal mineralogy. We suggest that the broad increase of aragonitic biota has been controlled by changes in atmospheric carbon dioxide partial pressure (pCO2) via carbonate mineral kinetics. Through the Phanerozoic, broadly decreasing pCO2 levels led to decreasing total alkalinity and dissolved inorganic carbon, and increasing oceanic pH. Superimposed upon this general trend, there are cyclic episodes of relatively high pCO2 and saturation state combined with a lower ratio of magnesium to calcium ions in seawater driven by the relatively slow changes in mid-ocean ridge expansion rates. Mass extinction events, many of which may have been caused by rapid global changes in temperature and/or pCO2, represent major intervals of turnover.