To examine the differentiation and transition of vascular system in Prunus davidiana FR., the mature embyro and developing seedlings were embedded in paraplast and treated by clearing method. In mature embryo, the procambium was connected with the epicotyl-hypocotyl-radicle axis and cotyledons, whereas protophloem and protoxylem were restricted primarily to the mid-vein and two lateral veins of the cotyledonary base. With the onset of germination, protophloem and protoxylem were differentiated both acropetally and basipetally from the cotyledonary base. The first and second leaf traces appeared in the cotyledonary node, and then differentiated bidirectionally toward the epicotyl and the root tip. The 3rd to 6th leaf traces were connected with the cotyledonary traces in hypocotyl. At the part of the root tip, the xylem was a diarch. As the first and second leaf traces were superimposed at the middle part of the root, the diarch xylem was changed to a tetrarch. As the cotyledonary traces were diverged below the root base, the tetrarch xylem was changed to an octarch. It was suggested that the vascular system of the epicotyl might be superimposed on that of the cotyledon-hypocotyl-root during the formation of the primary vascular system of Prunus davidiana.