Calcium-activated photoproteins are important and useful bioluminescent reagents for detecting the calcium ion (Ca2+) in biological systems. In conjunction with photon imaging technology, they can be used to observe Ca2+-related life processes in a living cell. To develop useful applications of calcium-activated photoproteins, we need to understand the molecular basis of the bioluminescence reaction. For this purpose, this review describes the oxygenation, chemiexcitation, and light emission processes of calcium-activated photoproteins in the bioluminescence reaction together with the fundamental chemistry of the luminous substrate, coelenterazine, based on recent results from mechanistic chemical studies of these primary processes. Finally, the whole reaction mechanism, including the active site structures of apoproteins, along with available information about the molecular mechanism and the crystallographic structures of calcium-activated photoproteins are summarized.