In retinal photoreceptors, the duration of G protein signalling is tightly regulated by the GTPase-activating protein RGS9-1. RGS9-1 is anchored to the disk membranes of photoreceptor outer segments by association with the membrane-spanning protein R9AP. Here we report the cloning of chicken R9AP from an inner ear cDNA library and the isolation of a murine R9AP cDNA from a retinal library. In the chicken, R9AP appears to be expressed in a variety of neuronal tissues, particularly in sensory cells including inner ear hair cells, photoreceptors, and dorsal root ganglion neurons. In the mouse, R9AP is detectable predominantly in photoreceptors, but it is also weakly expressed in other areas of the central nervous system. The expression of R9AP beyond photoreceptors led us to examine potential alternative roles for R9AP besides anchoring RGS9-1 and we found sequence homology and structural similarity of the protein with members of the SNARE protein family. Expression of chicken and mouse R9AP interfered with intracellular trafficking of an indicator protein in an in vitro assay, suggesting a more active role of the protein, possibly in targeting. GTPase-activating proteins to specific membranous compartments.