MicroRNAs (miRNAs) are important post-transcriptional modulators of gene expression, which have been implicated in many physiological and pathological processes. In this study, we found that miR-219 expressed since early segmentation stages (16s) in spinal cord and mid-, hindbrain in zebrafish using Northern blotting and whole mounts ISH technologies. Moreover, knockdown or overexpression of miR-219 led to specific embryonic defects. Furthermore, TUNEL assay showed that overexpression of miR-219 induced significant cell apoptosis in the head and tail of zebrafish. Our study suggested that miR-219 may play an important role in zebrafish embryonic development.