In this study, the authors investigated the distribution of Zn and Hg by using synchrotron micro X-ray fluorescence spectrum (SR-μXRF) along the growth circles of the golden-green and white pearls from Japanese Pinctada martensii. Both Zn and Hg concentrations represent the model of "low at first-high-low at last" along the growth rings in microscopic images of the pearl. SR-μXRF mapping images correspond to different periods:recuperating period, balanced period, and an abnormal high metabolism period between these two periods. The μ-XRF mapping data show a positive correlation of Zn and Hg:for the golden-green pearl, r=0.6; while for the white pearl, r=0.58, and the gold-green one has higher quality. Loading matrix of R type factors in the golden-green Japanese Pinctada martensii pearl reveals that the factors that influence element concentrations are biological growth support, environmental impact, and biomineralization. The fact that Zn has higher contribution to the factor of environmental impact reveals that Zn concentration depends on antagonism effect to a large extent. The results obtained by the authors have guiding significance for Pinctada martensii pearl culture.