The DNA amplified fragment length polymorphism (AFLP) fingerprinting approach was used to identify a shell color-linked marker in the noble scallop Chlamys nobilis Reeve. The marker B1f176 was linked completely to the gene for bright-orange shell color with no recombination in the progeny we sampled. This marker was amplified in bright-orange parents and all orange progeny, but was absent in all of the brownish purple progeny. Nevertheless, AFLP markers are not feasible for large-scale application. Thus, we converted B1f176 into a sequence-characterized amplified region (SCAR) marker that we designated as SCAR Orange-142. The marker Orange-142, like the AFLP band from which it was derived, amplified a robust band in only the bright-orange scallops, both in F1 and F2 families as well as in a test group obtained from a seafood market. These results indicate that Orange-142 is tightly linked to the gene for orange shell color. In all but 1 of 10 F2 families derived from bright-orange F0 grandparents, the observed frequencies of orange progeny were consistent with Mendelian ratios expected from a 1-locus 2-allele system in which the brownish purple genotype was recessive. This study is the first report of the genetic basis for shell color in C. nobilis. The identification of a shell color-linked marker in the noble scallop improves our understanding of shell color inheritance and may contribute to C. nobilis broodstock enhancement programs using marker-assisted selection.