Based on the observation that the tumor suppressor gene PTEN (phosphatase and tensin homolog) reduces regeneration after spinal cord injury (SCI) as evidenced in the PTEN knockout mouse, we have investigated the function of Ptena and Ptenb, the two zebrafish homologs of mammalian PTEN, in adult zebrafish after spinal cord injury with the aim to assess the contribution of the two zebrafish genes to functional recovery in an animal species that spontaneously recovers from central nervous system injury. Inhibition of Ptena expression by antisense morpholino (MO) application improved spinal cord regeneration through 4 to 5weeks after injury. Retrograde tracing showed regrowth of axons from neurons of the regeneration-competent nucleus of the medial longitudinal fascicle in the brainstem in the Ptena MO-treated fish. Ptenb MO-treated fish recovered as well as control MO-treated fish at 4 and 5weeks after SCI, with their locomotion being similar to that of sham-injured and non-injured fish. The mRNA levels of Ptena were upregulated after SCI at the early stage after injury (12h and 6days) caudal to the lesion site, compared to the non-injured control, while the levels of Ptenb were upregulated only at 12h after injury. In situ hybridization experiments were in agreement with the qPCR measurements. At the protein level, Ptena was found to be expressed in spinal motoneurons and immature neurons. These results indicate that Ptena, but not Ptenb, inhibits regeneration in zebrafish, thus sharing this feature with PTEN in mammals. The fact that zebrafish regenerate better than mammals despite the inhibitory presence of Ptena is likely due to regeneration-conducive molecules that tip the balance from inhibition to enhancement. Interestingly, although Ptena and Ptenb have been shown to be functionally redundant in promoting development of the fish larval central nervous system, they are not functionally redundant in the adult, suggesting that regeneration in fish is not predominantly due to overall recapitulation of development.