AbstractThe four visual sensory structures of a cubomedusa, the rhopalia, display a surprisingly elaborate organization by containing two lens eyes and four bilaterally paired pigment cup eyes. Peptides containing the peptide sequence Arg‐Phe‐NH2 (RFamide) occur in close association with visual structures of cnidarians, including the rhopalia and rhopalial stalk of cubomedusae, suggesting that RFamide functions as a neuronal marker for certain parts of the visual system of medusae. Using immunofluorescence we give a detailed description of the organization of the RFamide‐immunoreactive (ir) nervous system in the rhopalia and rhopalial stalk of the cubomedusae Tripedalia cystophora and Carybdea marsupialis. The bilaterally symmetric RFamide‐ir nervous system contains four cell groups and three morphologically different cell types. Neurites spread throughout the rhopalia and occur in close vicinity of the pigment cup eyes and the lower lens eye. Two commissures connect the two sides of the system and neurites of one rhopalial cell group extend into the rhopalial stalk. The RFamide‐ir nervous system in the rhopalia of cubomedusae is more widespread and comprises more cells than earlier discerned. We suggest that the system might not only integrate visual input but also signals from other senses. One of the RFamide‐ir cell groups is favorably situated to represent pacemaker neurons that set the swimming rhythm of the medusa. J. Comp. Neurol. 516:157–165, 2009. © 2009 Wiley‐Liss, Inc.