The objectives of this study were to 1) determine the influence of environmental factors (water temperature, food availability [chlorophyll-a], salinity) on nacre deposition rate and tablet thickness at different positions in shells of two strains of pearl oyster, Pinctada fucata (Gould, 1850)—one from Japan, and one a Hybrid between this Japanese strain and another from China; 2) compare nacre deposition rates and tablet thickness in different shell positions within and between these two pearl oyster strains; and 3) determine relationships between shell nacre deposition rate and tablet thickness in host oysters of these two strains with those of their pearls. Nacre and tablet thickness were measured at three positions along the mantle pallial line (anterior, middle, and posterior), and one position close to the hinge, on the left valve of each oyster. Water temperature and chlorophyll-a were positively correlated (p < .001, Spearman's rho >0.75) and salinity was negatively correlated (p < .001, Spearman's rho < −0.7) with nacre deposition rate at all shell positions in both pearl oyster strains. Only water temperature below 13 °C influenced nacre tablet thinning. Significant differences in total nacre deposition occurred between the four sampling positions on the shell in both strains (p < .001), with deposition at the hinge area the slowest for both Hybrid (373.212 μm) and Japanese (569.248 μm) oysters. Nacre tablet thickness in the middle position on the shell increased most steadily over time, and was thinnest in the coolest months (0.151 μm and 0.167 μm for Hybrid and Japanese oysters, respectively). No significant difference (p > .05) in nacre tablet thickness was apparent between strains. Correlation analysis of nacre deposition rate between the shell and pearls showed that all shell positions were highly correlated with their respective pearls (p < .001, Spearman's Rho >0.75). Environmental factors influence shell nacre deposition and thickness, and because shell nacre deposition is related to pearl nacre, pearl growth also. This influence varies in different shell positions, with nacre deposition in the posterior position on the shell the fastest, and the middle position showing the most stable and thin nacre tablet. Japanese pearl oysters exhibit better nacre deposition than Hybrid oysters and would be more appropriate as host oysters in Ago Bay, Japan, should culture occur in environmental conditions comparable to those in this study.