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The aim of this study was to compare total carotenoid content (TCC) in tissues, and its correlation with shell color between four different shell color strains of Pinctada fucata. A total of 120 individuals (30 golden shells, 30 red shells, 30 black shell and 30 white shells) of P. fucata of similar size were evaluated. In this study, stomach, gill, adductor, and mantle were used for measuring the determination of TCC. The color measurements were taken from both the nacre shells and cuticle shells. The results showed that TCC varies significantly among four different tissues and the four different shell color strains (P < 0.05). A significant difference between the cuticle shell colors of the four different shell color strains of P. fucata was observed (P < 0.05), while the nacre shell colors of four shell strains were similar (P > 0.05). In the present study, results indicated that the TCC of P. fucata was significantly related to tissue and cuticle shell colors (P < 0.001), but not related to nacre shell colors (P > 0.05). TCC relating to the cuticle shell color suggested that increasing or decreasing TCC in P. fucata through selective breeding of cuticle shell color was feasible, and it could be significant both for food for humans, and the cultivation of high-quality pearls.