Cerebral and spinal vascular systems are organized individually, and they then conjugate at their border, through the integration of basilar artery and vertebral arteries. Zebrafish (Danio rerio) is an ideal organism for studying early vascular development, and the precise procedure of cranial and truncal vascular formation has been previously demonstrated using this model. However, the stepwise process of the integration between the brain and spinal cord has not been clearly elucidated. In this study, we describe the integration of the independent vascular systems for the brain and spinal cord, using transgenic zebrafish expressing enhanced green fluorescent protein in endothelial cells. Initially, basilar artery and primordial hindbrain channels, into which internal carotid arteries supplied blood, were connected with dorsal longitudinal anastomose vessels, via the first intersegmental artery. This initial connection was not influenced by flow dynamics, suggesting that vascular integration in this region is controlled by genetic cues. Vertebral arteries were formed individually as longitudinal vessels beneath the spinal cord, and became integrated with the basilar artery during subsequent remodeling. Furthermore, we confirmed the basal vasculature was well conserved in adult zebrafish. Observations of vascular integration presented herein will contribute to an understanding of regulatory mechanisms behind this process.