We constructed the microsatellite-based linkage maps using 318 markers typed in two F(1) outbred families of Zhikong scallop (Chlamys farreri). The results showed an extremely high proportion (56.2%) of non-amplifying null alleles and a high ratio (30%) of segregation distortion. By aligning different individual-based linkage maps, 19 linkage groups were identified, which are consistent with the haploid chromosome number of Zhikong scallop. The integrated linkage map contains 154 markers covering 1561.8 cM with an average intermarker spacing of 12.3 cM and 77.0% of genome coverage. We found that the heterogeneity in recombination rate was not determined by sexes but by different individuals on 18 linkage regions. The phenotypic marker of general shell colour was placed on LG4, which was flanked by microsatellite markers CFLD064 and CFBD055. Four size-related traits including shell length (SL), shell width (SW), shell height (SH) and gross weight (GW) were analysed to identify the putative quantitative trait loci (QTL). Under the half-sib model, using dam as common parent, three, two, two and one QTL affecting SL, SW, SH and GW exceeded the genome-wide thresholds respectively. While using sir as common parent, a larger number of QTL were detected for these four traits: four, five, three and two for SL, SW, SH and GW respectively. The single QTL explained 3.7-19.2% of the phenotypic variation. The linkage map and the QTL associated with economic traits will provide useful information for marker-assisted selection of Zhikong scallop.