Zebrafish express in their retina a higher number of guanylate cyclase-activating proteins (zGCAPs) than mammalians pointing to more complex guanylate cyclase signaling systems. All six zGCAP isoforms show distinct and partial overlapping expression profiles in rods and cones. We determined critical Ca(2+)-dependent parameters of their functional properties using purified zGCAPs after heterologous expression in E.coli. Isoforms 1-4 were strong, 5 and 7 were weak activators of membrane bound guanylate cyclase. They further displayed different Ca(2+)-sensitivities of guanylate cyclase activation, which is half maximal either at a free Ca(2+) around 30 nM (zGCAP1, 2 and 3) or around 400 nM (zGCAP4, 5 and 7). Zebrafish GCAP isoforms showed also differences in their Ca(2+)/Mg(2+)-dependent conformational changes and in the Ca(2+)-dependent monomer-dimer equilibrium. Direct Ca(2+)-binding revealed that all zGCAPs bound at least three Ca(2+). The corresponding apparent affinity constants reflect binding of Ca(2+) with high (≤ 100 nM), medium (0.1-5 µM) and/or low (≥ 5 µM) affinity, but were unique for each zGCAP isoform. Our data indicate a Ca(2+)-sensor system in zebrafish rod and cone cells supporting a Ca(2+)-relay model of differential zGCAP operation in these cells.