To study the effects of connexin43 down regulation on the development of the embryonic heart and vasculature in zebrafish, two types of well designed morpholino oligonucleotide antisenses were injected into zebrafish embryos to block the translation of cx43 at one or two cells stage. After injection, the phenotypes of heart and vasculature were monitored by whole mount in situ hybridization, whole-mount immunofluorescence and microangiography. Whole-mount in situ hybridization with vmhc and amhc RNA probes showed that the vmhc expression cell domain was reduced; meanwhile, amhc expression cell domain was increased in cx43 down regulation group. Whole-mount immunofluorescence provided the evidence that down regulation of cx43 resulted in enlarged atrium and retrenched ventricle. Both in situ hybridization and microangiography indicated that vasculature pattern of cx43 morphants are almost normal compared with wildtype. Besides, the function of heart was affected obviously. Down regulation of cx43 caused the development defects of zebrafish embryonic heart, which may be involved in the wrong destination of two migratory cell populations, but it did not nearly affect vascular development.