Cyanobacterial calcification is promoted by CO2-concentrating mechanisms (CCMs) developed in response to photosynthetic carbon limitation. Changes in atmospheric composition (CO2 fall, O2 rise) near the Devonian–Mississippian transition (ca. 360 Ma) were sufficiently large to induce CCMs in cyanobacteria. Cyanobacterial sheath calcification significantly increased during the Mississippian, ca. 325–355 Ma. It is proposed that these atmospheric changes triggered cyanobacteria to induce CCMs—previously developed during a large CO2 decline in the Proterozoic—and that this promoted their calcification. CCMs in phytoplankton stimulate primary productivity by increasing photosynthetic efficiency and ameliorating carbon limitation. Phytoplankton community restructuring in favor of groups that possessed effective CCMs but had poor body-fossil records, such as picoplanktic cyanobacteria, could account for Late Devonian acritarch decline and the subsequent apparent scarcity of phytoplankton in the late Paleozoic (the so-called phytoplankton blackout). This is supported by biomarkers indicating an increase in cyanobacteria at the Devonian–Mississippian transition and by carbon isotope values and black shale deposition that, despite acritarch decline, reflect increased primary productivity. The Mississippian episode of cyanobacterial calcification was relatively short lived. Calcification declined ca. 325 Ma, before the end of the Mississippian, as a continued decline in CO2 lowered seawater carbonate saturation. The induction of cyanobacterial CCMs, triggered by Late Devonian change to a relatively low CO2 and high O2 atmosphere, has probably persisted to the present day, but well-developed calcification in marine cyanobacteria has been restricted to intervals of elevated carbonate saturation state.