A common feature of animal locomotion is its organization into gaits with distinct patterns of movement and propulsor use for specific speeds. In terrestrial vertebrates, limb gaits have been extensively studied in diverse taxa and gait transitions have been shown to provide efficient locomotion across a wide range of speeds. In contrast, examination of gaits in fishes has focused on axial gaits and the transition between synchronous paired fin locomotion and axial propulsion. Because many fishes use their pectoral fins as their primary propulsors, we aimed to examine more broadly the use of pectoral fin gaits in locomotion. We used juvenile reef fishes in these experiments because their swimming could be recorded readily across a wide range of Reynolds numbers, which we thought would promote gait diversity. Based on previous work in larval fishes, we hypothesized that juveniles have alternating pectoral fin movements rather than the synchronous, or in-phase, coordination pattern of adults. In flow tank swim studies, we found that juvenile sapphire damselfish Pomacentrus pavo used two fin gaits during steady swimming. Below approximately 3 BL s(-1), P. pavo primarily swam with alternating fin strokes 180 degrees out of phase with one another. At speeds in the range of 3-4 BL s(-1), they performed a gait transition to synchronous fin coordination. Between approximately 4 and 8 BL s(-1), P. pavo primarily beat their fins synchronously. At around 8 BL s(-1) there was another gait transition to body-caudal fin swimming, in which the pectoral fins were tucked against the body. We suggest that the transition from alternating to synchronous fin coordination occurs due to mechanical limits of gait performance rather than to energy efficiency, stability or transitions in hydrodynamic regime. To determine whether this gait transition was species-specific, we surveyed pectoral fin locomotion in juveniles from 11 species in three reef fish families (Pomacentridae, Labridae and Scaridae). We found that this gait transition occurred in every species examined, suggesting that it may be a common behavior of juvenile reef fishes. Greater inclusion of early life history stages in the study of fin-based locomotion should significantly enhance and inform the growing body of work on these behaviors.