The second messengers 3′,5′-cyclic adenosine monophosphate (cAMP) and cyclic 3′,5′-cyclic guanosine monophosphate (cGMP) mediate various biological responses like apoptosis, smooth muscle relaxation and vision. Cyclic-nucleotide-dependent processes have been analyzed with spatiotemporal resolution through optogenetics. In particular, genetically encoded light-activated nucleotidyl cyclases have been employed to synthesize cAMP and cGMP in living cells and organisms. For example, the fungal rhodopsin-guanylyl cyclase RhGC was shown to induce light-dependent cGMP signaling in neurons. The complementary light-controlled breaking of cAMP and cGMP has been achieved through the synthetic light-activated phosphodiesterase (LAPD) only. Yet, no natural phosphodiesterase is known that catalyzes the degradation of cyclic nucleotides in a light-dependent manner. However, microbial genome and transcriptome mining lead to the emergence of natural light-activated phosphodiesterase candidates. Here we describe a natural rhodopsin-coupled phosphodiesterase (RhPD) from a flagellar protist. The final goal of this study is the isolation of a light-activated RhPD. A functional RhPD could allow optogenetic analysis of diverse cGMP/cAMP-mediated and membrane located processes in cells and vertebrate model organisms.