Ctenogobiops is a genus of Indo-Pacific gobies that form obligate, mutualistic associations with shrimp in the genus Alpheus. This study provides a molecular phylogenetic analysis of eight Ctenogobiops species: C. aurocingulus, C. crocineus, C. feroculus, C. formosa, C. maculosus, C. mitodes, C. tangaroai, and C. tongaensis. We recover two clades within the genus, one consisting of C. feroculus and C. aurocingulus, the second including the remaining species arrayed as follows: (C. tongaensis (C. mitodes (C. formosa (C. maculosus (C. crocineus, C. tangaroai))))). Recovery of C. maculosus and C. crocineus as distinct taxa suggests that these species are not synonymous, although sampling in this study is limited. Species of Ctenogobiops are morphologically very similar to each other, with generally consistent meristic character states present throughout the genus. Recognition of species is based primarily on slight variations in color pattern, shape of the dorsal fin, and size of the gill opening. Comparison of our specimens of C. mitodes with accounts of C. pomastictus confirms that color pattern variations and lateral scale counts are more reliable indicators of species identity than relative dorsal fin spine length, particularly for smaller specimens. We evaluate the distribution of morphological characters in the context of the new phylogenetic hypothesis, and provide a summary of distinguishing characters for Ctenogobiops species. In this case, as in other instances of diverse reef-dwelling fish taxa, molecular data are ideal for inferring phylogenetic relationships, whereas morphological data remain the most expedient way to identify species.