Modulation of Ca(2+) within cells is tightly regulated through complex and dynamic interactions between the plasma membrane and internal compartments. In this study, we exploit in vivo imaging strategies based on genetically encoded Ca(2+) indicators to define changes in perikaryal Ca(2+) concentration of intact photoreceptors. We developed double-transgenic zebrafish larvae expressing GCaMP3 in all cones and tdTomato in long-wavelength cones to test the hypothesis that photoreceptor degeneration induced by mutations in the phosphodiesterase-6 (Pde6) gene is driven by excessive [Ca(2+)]i levels within the cell body. Arguing against Ca(2+) overload in Pde6 mutant photoreceptors, simultaneous analysis of cone photoreceptor morphology and Ca(2+) fluxes revealed that degeneration of pde6c(w59) mutant cones, which lack the cone-specific cGMP phosphodiesterase, is not associated with sustained increases in perikaryal [Ca(2+)]i. Analysis of [Ca(2+)]i in dissociated Pde6β(rd1)mouse rods shows conservation of this finding across vertebrates. In vivo, transient and Pde6-independent Ca(2+) elevations ('flashes') were detected throughout the inner segment and the synapse. As the mutant cells proceeded to degenerate, these Ca(2+) fluxes diminished. This study thus provides insight into Ca(2+) dynamics in a common form of inherited blindness and uncovers a dramatic, light-independent modulation of [Ca(2+)]i that occurs in normal cones.