Intra-aortic haematopoiesis is a transient phenomenon, present in all the vertebrate species examined. Aorta-associated haematopoiesis produces Haematopoietic Stem Cells (HSC) that emerge from the ventral aortic endothelium through endothelial cells (EC) that switch to HSC. HSC emergence is followed by the colonization of definitive haematopoietic organs. Since intra-aortic haematopoiesis is born from EC of the aortic floor, we wondered how vascular integrity was maintained during haematopoietic production. Transplantation experiments have brought about evidence according to which two distinct endothelial lineages contribute to the embryonic vasculature. One comes from the splanchnic mesoderm and gives rise to EC and haematopoietic cells (HC). The other originates from the somite and is restricted to EC differentiation. We have used interspecific quail/chick grafts to study aortic organogenesis during the course of haematopoiesis. We demonstrate that: 1) before haematopoiesis, the aorta, originally entirely of splanchnic origin, is colonized by EC from the somite. This colonization contributes to create a new roof and sides, which are hence formed by somite-derived EC whereas the floor is contributed by splanchnopleural-derived EC; 2) as haematopoiesis proceeds, somite-derived EC begin to colonize the aortic floor and are found beneath HSC clusters; 3) after haematopoiesis, aortic hemangioblasts disappear from the endothelium and are replaced by somite-derived EC. At this stage, the whole aortic endothelium is derived from somitic cells; 4) we have identified a new cell population from the somite that contributes to the vascular smooth muscle cells (VSMC). This population appears distinct from the somite-derived EC. Using lineage tracing with non-replicative retroviral vectors, we show that EC do not give rise to VSMC as previously thought. Taken together, our results bring about new lights on aorta morphogenesis and the time-restricted production of haematopoiesis.