Objective To investigate the role of pcgf5a gene during zebrafish embryonic development.   Methods pcgf5a morpholine antisense morpholino oligomers(MO) was microinjected to delete the expression of pcgf5a gene, and possible phenotypes were examined in pcgf5a-deficient embryos. The whole mount in situ hybridization and Real-time PCR were used to detect alterations of key genes related to the development of nervous system and eye.   Results After pcgf5a gene knockdown, the development of ectoderm and mesoderm of zebrafish embryos were affected. The brain size became smaller, and the eyes developed retarded, and the tail was curled and the body axis was shortened（548/891）. In addition, the expressions of sox2(82/98), sox3（73/84）, foxg1（70/88）, pax6a（36/45）, pax2a, vsx2 and rx1(n=5) were significantly reduced.   Conclusion pcgf5a affects the morphogenesis of nervous system and eye, possibly due to regulating the expression of the transcription factors related to their development via the processes of cell proliferation and apoptosis.