Genetic linkage maps were constructed for the noble scallop Chlamys nobilis Reeve on the basis of 373 amplified fragment length polymorphisms (AFLPs) and 9 microsatellite markers. The pseudo test-cross mapping strategy was used to construct the maps. The female linkage map contained 117 (115 AFLPs and 2 microsatellites) markers spanning 1,698.6 cM, with an average interval of 16.8 cM. The male linkage map had 108 markers (106 AFLPs and 2 microsatellites) covering 1,519.0 cM, at 16.5 cM per marker. Sixteen linkage groups were identified in both maps, which were consistent with the 16 chromosomes seen in chromosome spreads. The genetic length of the C. nobilis genome was estimated to be 2,235.1 cM for the female and 2,053.5 cM for the male. The observed coverage was 76.0% for the female map and 74.0% for the male map. When triplets and doublets were considered, the observed length of the map was calculated to be 2,002.1 cM with coverage of 89.6% for the female and 1,864.2 cM with coverage of 90.8% for the male. The genetic maps presented here will serve as a preliminary groundwork for the construction of a high-resolution genetic map of C. nobilis.