Gobies (family Gobiidae) have a complex mechanosensory lateral line system characterized by reduced lateral line canals and a dramatic proliferation of small superficial neuromasts (on ‘‘sensory papillae’’), which are arranged in lines on the head, trunk, and tail. A suite of morphological methods was used to describe the distribution and morphology of canal and superficial neuromasts in the neon goby, Elacatinus lori, and to describe the ontogeny of the lateral line system for the first time for any gobiiform fish. Portions of only three cranial lateral line canals are retained and they contain a total of eight canal neuromasts. In addition, 128–155 superficial neuromasts are found in six head series (comprising 33 neuromast lines or rows). Superficial neuromasts are found in one body series (65–80 neuromasts arranged in three groups of vertical lines or ‘‘stitches’’) and one caudal fin series (3 lines, each located between fin rays and comprised of many small neuromasts; total of 27–53 neuromasts) extending to the tip of the caudal fin. The general distribution of neuromasts is established early during the larval stage, and neuromast numbers increase within and among lines resulting in an increase in overall complexity of the system. On day-of-hatch, a total of 22 neuromasts are present. At~15 days post-hatch, all eight cranial canal neuromasts are present, and, in post-settlement juveniles (‘‘settlers’’), they are enclosed in canals and a total of ~185 neuromasts are found on the head, trunk, and tail. All neuromasts are small (~40 lm long) and diamond-shaped, but three subpopulations (canal neuromasts, canal neuromast homologs, superficial neuromasts) are defined based on their location and their arrangement within lines (‘‘tip-to-tip’’ or ‘‘side-byside’’). The ontogeny of the lateral line system and distinctions among neuromast subpopulations help to reveal the structural and functional organization of the complex lateral line system in Elacatinus and will contribute to the interpretation of neuromast patterns in other gobiiforms. A comparison of superficial neuromast number in 12 species of Elacatinus and Tigrigobius (sister genera) revealed variation among species that live in different reef microhabitats, which suggests that adaptive evolution in the lateral line system is evident among closely related taxa.