Abstract: Objective The aim of this study was silence Pitx2 gene by Pitx2- morpholino oligos microinjection so as to explore the effect of down-regulated Pitx2 on tooth development related genes in zebrafish. Methods Pitx2 gene was down-regulated by morpholino oligos microinjection. We observed the development of the embryos in 72 hours with microscopes, synthesized gene probes for Bmp4、Fgf8 by cloning specific gene fragment of Bmp4 and Fgf8 with RT-PCR directly，and then carried out the in situ hybridization with embryos from different stages during early dental development to observe the effect of down-regulated Pitx2 on expression of Bmp4 and Fgf8 in zebrafish branchial arch in early dental development. Results We successfully synthesized gene probes for Bmp4 and Fgf8，and observed the development of the embryos in 72 hours with microscopes. Growth retardation or termination,. pericardial edema, spinal and eyes deformity appeared in the zebrafish embryos in Morpholino groups after Pitx2- morpholino oligos microinjection. In situ hybridization showed that down-regulated Pitx2 increased the expression of Bmp4, and repressed the expression of Fgf8 in branchial arch of zerafish after Pitx2- morpholino oligos microinjection, compared with wild zebrafish. Conclusion We found out the Effect of down-regulated Pitx2 on the early dental development related genes Bmp4 and Fgf8 in zebrafish.