Carotenoid is an important economic trait for genetic and breeding in animals and plants. The noble scallop Chlamys nobilis is an important aquaculture bivalve in southern China. Studies in the noble scallop have shown that carotenoids content among individuals in their muscle are varies. In order to explain the variation, a genetic map was constructed in this study using F₂ progenies with different carotenoids content, and then QTLs for carotenoids content in adductor and mantle were analyzed. Totally, 225 polymorphic markers (170 SNPs, 32 InDels and 23 SSRs) were developed from expressed sequence tags (ESTs). The female map had 16 linkage groups and spanned 595.2 cM with an average interval of 6.7 cM, and the male map had 19 linkage groups and spanned 745.7 cM with an average interval of 7.2 cM. However, the integrated map only contained 14 linkage groups, spanning 691.2 cM and with an average interval of 4.8 cM. A total of five QTLs were identified including three in the adductor and two in the mantle, which were distributed in linkage group 1 (Z1), 5 (Z5) and 12 (Z12), respectively. In addition, two QTLs on Z12 completely overlapped, which explained 28.0% in the adductor and 55.6% in the mantle of phenotypic variation, respectively, suggesting the presence of important carotenoid-determining genes in this region. The present study was the first to construct a genetic map using animals with different carotenoids content and identified five QTLs for carotenoids content, which can provide new insights for further understanding genetic mechanism of carotenoids deposition.