We have cloned a cDNA encoding a putative cyclic nucleotide-gated (CNG) channel from Drosophila melanogaster. The N-terminal half of the predicted protein, designated as CNGL, shows a high degree of sequence similarity with the known CNG channel proteins. CNGL has a long hydrophilic C-terminal stretch that is absent in other CNG channels. Northern blot analysis revealed that the messenger RNA (mRNA) corresponding to the size of the cloned cDNA is expressed in Drosophila heads. Immunolocalization studies showed that CNGL is expressed in the brain, including the medulla, lobulla and lobulla plate, the antennal lobe glomeruli, and mushroom bodies. These results suggest a possible role of the putative CNGL channel in the processing of visual and olfactory information in the nervous system of Drosophila.