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Shell color polymorphism is common in nature for the marine mollusks. The Pacific oyster Crassostrea gigas , is widely cultured and one of the most economically important bivalve species with various shell color variants. Here, a total of 1061 single nucleotide polymorphism markers, developed from expressed sequence tags (EST-SNPs), were used to construct two genetic linkage maps based on reciprocal-cross between black shell and white shell oysters (MF-A and MF-B) respectively. The two separate linkage maps were combined into an integrated map spanning 947.31 cM in total length. The integrated map was composed of 351 EST-SNP markers distributing on 10 linkage groups, with an average interval of 2.78 cM between adjacent markers. For the MF-A, 11 quantitative trait loci (QTLs) for shell color traits and five QTLs for growth traits were detected, explaining 8.1%–13.8% (mean = 11.76%) and 10.4%–11.0% (mean = 10.66%) phenotypic variance respectively. For the MF-B, nine QTLs for shell color traits and eight QTLs for growth traits were detected, explaining 8.8%–21.7% (mean = 12.84%) and 8.4%–9.4% (mean = 8.88%) phenotypic variance respectively. QTLs clustering was found on the linkage group 2 of the MF-A and the linkage group 8 of the MF-B, and the QTLs showed that pleiotropism could affect at most three traits. Three shared-QTLs associated with shell color traits were identified on the integrated map, and one of them (qA- a * 4) was significantly homologous to C. gigas calmodulin-like protein. The QTLs identified in the present study could be useful in finding candidate genes for the shell color and growth-related traits in future, and potentially applied to marker-assisted selection breeding programs for C. gigas . [ABSTRACT FROM AUTHOR]