Marker-assisted selection is commonly used to find molecular markers or genes associated with economic traits that are often controlled by multiple genes and inherited as quantitative traits. Eye diameter (ED) and eye cross (EC) are two of the most important quantitative traits in common carp. They are also important morphological characteristics often used in fish taxonomy. We used a full-sib family (68 individuals) of hybrid mirror carp ( L.) to analyze the correlation between 164 microsatellite markers, obtained from a bacterial artificial chromosome (BAC), with ED and EC. We obtained 401 alleles and 463 genotypes from the 164 markers. We used a general liner model with permutation test (10 000 times) to evaluate the relationship between the genotypes and the two traits. Twenty-two of the SSR markers had significant correlation with ED and/or EC(0.05). Six SSR markers, including CAFS1526, were significantly correlated with ED(0.05) and 11 SSR markers, including CAFS0882, were significantly correlated with EC(0.05), and CAFS1298 and CAFS1423 were highly significantly correlated with both ED and EC(0.01). The genotypes at each marker related to the two traits were obtained using Duncan’s multiple comparison test. The markers significantly related to ED and EC were assigned to a linkage map, and nine markers were consistent with the QTL mapping for ED or EC, which explained 13.3–20.9% of the phenotypic variance. These functional markers from the BAC and its genotypes may be used for both MAS and constructing an integrated linkage map with a physical map of the common carp.