A common carp gynogenetic line including 44 individuals derived from the cross Barbless carp × Hebao-cold tolerance red carp was used to construct a linkage map using 445 markers (265 AFLP markers, 127 SSR markers, 37 EST-SSR markers and 16 RAPD markers). Quantitative traits loci (QTLs) associated with head length, eye diameter, and eye cross were identified by composite interval mapping of the software WinQTLCart2.5. Five QTLs were identified for head length on the linkage group of LG2, LG3,

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... 40, and LG4, which explained 12.39% to 34.29% of the total variation of the head length. All of their additive effects were negative. Two QTLs were associated with eye diameter on the linkage groups of LG39 (qED-39-1) and LG40 (qED-40-1), which explained 9.77% and 5.62% of the total variation of the eye diameter, respectively. The additive effect of qED-39-1 was positive and that of qED-40-1 was negative. Two QTLs were responsible for eye cross on the linkage group of LG28 and LG20, explaining 8.88% and 8.29% of the total variation of the eye cross, respectively. The additive effect of qEC-28-1 was negative and that of qEC-20-1 was positive.