The F1 progeny from parents selected randomly for differences in performance traits from different families of mirror carp were used as a mapping panel. Linkage maps constructed using Join Map 4.0 software with 992 microsatellite polymorphic markers ultimately yielded 51 groups. Composite interval mapping (CIM) of superoxide dismutase (SOD) trait of three tissues (liver, anterior and posterior intestine) was conducted for quantitative trait loci (QTL) location using Map QTL 6.0 software. Results shows that seven QTLs significantly (P < 0.05) explained 8.2–18.5% of the phenotypic variations in liver, five QTLs explained 7.9–11.1% of the variation in anterior intestine (P < 0.05) and six QTLs were located and explained 6.1–15.8% of the phenotypic variations in posterior intestine (P < 0.05). NCBI BLASTn was used for homology analysis between the sequences from markers used in the located QTL regions and sequences from the zebrafish database, and many protein relating with the SOD expression were blasted (similarity >85%). These results showed that it is highly probable that these QTLs are the main regions of SOD expression. The data also support the value of forward genetic studies on organism development and serve as a basis for selection.