Polysialic acid (PSA) is a developmentally regulated carbohydrate attached to the neural cell adhesion molecule (NCAM). PSA is involved in dynamic processes like cell migration, neurite outgrowth and neuronal plasticity. In mammals, polysialylation of NCAM is catalyzed independently by two polysialyltransferases, STX (ST8Sia II) and PST (ST8Sia IV), with STX mainly acting during early development and PST at later stages and into adulthood. Here, we functionally characterize zebrafish Stx and Pst homolog genes during fish development and evaluate their catalytic affinity for NCAM in vitro. Both genes have the typical gene architecture and share conserved synteny with their mammalian homologues. Expression analysis, gene-targeted knockdown experiments and in vitro catalytic assays indicate that zebrafish Stx is the principal--if not unique--polysialyltransferase performing NCAM-PSA modifications in both developing and adult fish. The knockdown of Stx exclusively affects PSA synthesis, producing defects in axonal growth and guidance. Zebrafish Pst is in principle capable of synthesizing PSA, however, our data argue against a fundamental function of the enzyme during development. Our findings reveal an important divergence of Stx and Pst enzymes in vertebrates, which is also characterized by a differential gene loss and rapid evolution of Pst genes within the bony-fish class.