The chemical compositions and component distributions of Pinctada martensii pearls from Japan were investigated by synchrotron X-ray fluorescence spectrum. The results clearly show that these pearls contain Ca, Sr, Ba alkaline-earth metal elements, Mn, Fe, Cu, and Zn 3d transition metal elements and rare earth elements. In pearls, these elements present some distributions in space: the nucleus surface has the highest concentrations of rare earth elements and the concentrations of rare earth elements in the nacre and nucleus are roughly equal; in the nucleus there exists decreasing tendency of elements Mn and Fe from the superficial part to the surface; both Mn and Fe exhibit sharp fall in the same circle of the nacre, showing a certain correlation, and the place of sharp fall seems to be the dividing line of nacreous layer and prismatic layer; element Mn mainly exists in prismatic layer; the distributions of elements Sr and Ba show negative relationship with element Ca.