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Centrins are Ca2+-binding EF-hand proteins. All four known centrin isoforms are expressed in the ciliary apparatus of photoreceptor cells. Cen1p and Cen2p bind to the visual G-protein transducin in a strictly Ca2+-dependent way, which is thought to regulate light driven movements of transducin between photoreceptor cell compartments. These relatively slow motile processes represent a novel paradigm in light adaptation of photoreceptor cells. Here we validated specific phosphorylation as a novel regulator of centrins in photoreceptors. Centrins were differentially phosphorylated during photoreceptor dark adaptation. Inhibitor treatments revealed protein kinase CK2 as the major protein kinase mediating phosphorylation of Cen1p, Cen2p and Cen4p, but not Cen3p, at a specific target sequence. CK2 and ciliary centrins co-localize in the photoreceptor cilium. Direct binding of CK2 and centrins to ciliary microtubules may spatially integrate the enzyme-substrate specificity in the cilium. Kinetic light-scattering assays revealed decreased binding affinities of phosphorylated centrins to transducin. Furthermore, we show that this decrease is based on the reduction of Ca2+-binding affinities of centrins. Present data describe a novel regulatory mechanism of reciprocal regulation of stimulus dependent distribution of signaling molecules.