The molecular basis of lymphangiogenesis remains incompletely characterized. Here, we document a novel role for the PDZ domain-containing scaffold protein synectin in lymphangiogenesis using genetic studies in zebrafish and tadpoles. In zebrafish, the TD arises from parachordal lymphangioblast (PL) cells, which in turn derive from secondary lymphangiogenic sprouts from the posterior cardinal vein (PCV). Morpholino knockdown of synectin in zebrafish impaired formation of the thoracic duct (TD), due to selective defects in lymphangiogenic but not angiogenic sprouting. Synectin genetically interacted with Vegfr3 and neuropilin-2a in regulating lymphangiogenesis. Silencing of synectin in tadpoles caused lymphatic defects due to an underdevelopment and impaired migration of Prox-1(+) lymphatic ECs (LECs). Molecular analysis further revealed that synectin regulated Sox18-induced expression of Prox-1 and VEGFC-induced migration of LECs in vitro. These findings reveal a novel role for synectin in lymphatic development.