population consisting of 94 individuals to construct a linkage map for Jian carp using 254 microsatellite markers. We identified 17 quantitative trait loci for body length, body height, and body thickness on 10 linkage groups (LG), which explained 10.8%–35.2% of the phenotypic variance. Comparative mapping between Jian carp and mirror carp was used to assess the homology of quantitative trait loci for growth traits based on the same markers. A comparative analysis revealed extensive synteny or collinearity between the two varieties and each Jian carp LG showed homology towards a single mirror carp LG, sharing two or more loci with mirror carp LG in most cases. Ten QTLs for growth traits in Jian carp were conserved compared with 13 QTL for the same traits in mirror carp, accounting for 58.8% of the total. The QTL confidence interval in mirror carp was more precise than the homologous interval in Jian carp, which was generally contained within the QTL interval in Jian carp. Of note, we observed QTL rich regions on the LG in Jian carp and mirror carp, where QTL affecting different traits were generally clustered. The orthologous rich regions between the two varieties may represent “hot spots” for marker assisted selection. The detection of consensus QTL provides a basis for marker assisted breeding and fine mapping in carp.