The crystal structures of calcium‐loaded apoaequorin and apo‐obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF‐hand loops that have the canonical calcium‐binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium‐loaded apo‐proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2‐hydroperoxycoelenterazine, and also the same as the Ca2+‐discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.