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Abstract Swimming in schools has long been hypothesized to allow fish to save energy. Fish must exploit the energy from the wakes of their neighbors for maximum energy savings, a feat that requires them to both synchronize their tail movements and stay in certain positions relative to their neighbors. To maintain position in a school, we know that fish use multiple sensory systems, mainly their visual and flow sensing lateral line system. However, how fish synchronize their swimming movements in a school is still not well understood. Here we test the hypothesis that this synchronization may depend on functional differences in the two branches of the lateral line sensory system that detects water movements close to the fish’s body. The anterior branch, located on the head, encounters largely undisturbed free-stream flow, while the posterior branch, located on the trunk and tail, encounters flow that has been affected strongly by the tail movement. Thus, we hypothesize that the anterior branch may be more important for regulating position within the school, while the posterior branch may be more important for synchronizing tail movements. Our study examines functional differences in the anterior and posterior lateral line in the structure and tail synchronization of fish schools. We used a widely available aquarium fish that schools, the giant danio, Devario equipinnatus. Fish swam in a large circular tank where stereoscopic videos recordings were used to reconstruct the 3 D position of each individual within the school and to track tail kinematics to quantify synchronization. For one fish in each school, we ablated using cobalt chloride either the anterior region only, the posterior region only, or the entire lateral line system. We observed that ablating any region of the lateral line system causes fish to swim in a “box” or parallel swimming formation, which was different from the diamond formation observed in normal fish. Ablating only the anterior region did not substantially reduce tail beat synchronization but ablating only the posterior region caused fish to stop synchronizing their tail beats, largely because the tail beat frequency increased dramatically. Thus, the anterior and posterior lateral line system appear to have different behavioral functions in fish. Most importantly, we showed that the posterior lateral line system played a major role in determining tail beat synchrony in schooling fish. Without synchronization, swimming efficiency decreases, which can have an impact on the fitness of the individual fish and group.