Ordovician diorite-quartz diorite mylonite (Saganoseki quartz diorite) was discovered in Sambagawa metamorphic terrane at the north margin of Saganoseki Peninsula, Kyushu Island, Japan. The LA-ICP-MS zircon U–Pb geochronology revealed that the intrusion age of Saganoseki quartz diorite was 473.3 ± 3.6 Ma. These rocks show the volcanic arc affinity based on the trace element composition. On the basis of geochronological and geochemical results, Saganoseki quartz diorite is considered to be a member of the Early Paleozoic igneous rocks of the Kurosegawa tectonic zone. Saganoseki quartz diorite is located just south of the Median Tectonic Line (MTL) and is in close contact with the pelitic and psammitic schist without any brittle shear zone. U–Pb ages of detrital zircon grains from two psammitic schists show the estimated sedimentation age of early Late Cretaceous, indicate that these psammitic schists are the member of Sambagawa metamorphic rocks. Together with these results and the mode of occurrence in the field, we argue that the Early Paleozoic igneous rocks of the Kurosegawa tectonic zone existed as an upper structural unit of the Sambagawa terrane. This relationship is the key to reconstruct the Mesozoic tectonics of Japan as a part of East Asia, and its evolution through time.