Abstract: In this research, three polymorphic repetitive sequences and three SNPs in the Coja-DMB2 and Coja-B genes were identified in the quail Mhc (Coja) region using a total of six quails derived from two lines (HTUA and LTUA lines), which were selected by plasma IgG concentration. Subsequently, polymorphism and haplotype analyses were performed on these five polymorphic markers using 39 individuals of both lines. As a result, 11 kind of Coja haplotypes were predicted. Especially, from the frequencies of Coja haplotypes the haplotype 2, 3 and 10 have difference (P=0.028) between both lines.