The bacterium Cynoglossus semilaevis aquaculture industry. The fundamental approach has been to cultivate a new disease-resistant strain by combining traditional breeding methods with molecular techniques. In this study, bulked segregant analysis and quantitative trait loci (QTL) mapping were used to screen for disease-resistance markers. A total of 100 individuals were selected to form the F1412 family (nomenclature rule:F+year+family number:survival rate, 52.22%), which was challenged with , and 169 microsatellite loci were detected across all chromosomes. Following the genomic scan, the scaffold479_23523 marker in the DNA pool was significantly different between the resistant and susceptible groups (=0.000006). Ninety-four individuals were genotyped using all 32 simple sequence repeat markers on LG18, where scaffold479_23523 was located. Three new linkage groups (LG18, LG18F, and LG18M) were identified. Furthermore, two different analytical models were applied to perform a single marker analysis and composite interval mapping with different levels of significance in LG18, LG18F, and LG18M, respectively. In model 1, three significant markers (scaffold4475_71287, scx9-1, and cyse80) and one very significant marker (scaffold080437) were identified, and the qE-F1 resistance-related QTL was detected. The scaffold479_23523 marker was the left LG18F marker with a p-value of 0.0516 in model 1. Model 2 detected four significant markers (hncyse110, scaffold414_19940, scaffold4475_71287, and cyse80), one very significant marker (scaffold08043), and the qE-M1 and qE-M2 QTLs. Both scaffold080437 markers were significantly different (<0.001) in the two models. Four markers (scaffold080437, scaffold479_23523, scaffold4475_71287, and cyse80) may be closely associated with resistance to . qE-F1 explained 87.36% of the phenotypic variance and contained G18M qE-M1 and qE-M2. Thus, qE-F1 was considered a major candidate region for genome, three immunity-related genes, such as meteorin-like, the WD repeat domain phosphoinositide interacting 2, and Toni beta-propeller repeat containing 1, were detected inside qE-F1. This is the first study to identify resistance-related markers and conduct a related QTL analysis in . These results provide a foundation for selective breeding of disease-resistant .