This study was carried out to investigate the effects of selection on the single nucleotide polymorphisms (SNPs) in coding sequence of leptin receptor (LEPR) gene and possible associations between SNPs’ and some meat yield traits of Japanese quail lines. Fifteen generations divergently selected two lines (HBW and LBW) for 5-weeks of age body weight and a control were used as materials for this study. A 348-bp part of the LEPR coding region (18th exon) were sequenced in a total of 113 individuals from the three quail lines and shown that the fragments contained four SNPs loci (T490C, C528T, G537A, T571C) and five haplotypes (TTGT, CTGT, TCGT, TCAT, TCAC). T490C replacement caused the missense mutation of phenylalanine to convert to leucine (Phe>Leu). However, other SNPs were synonymous and there were no changes in transcripts. It was determined that the quails with higher phenotypic values were in the TT genotype at the T390C locus. Statistical analyses showed that there were significant differences among the quail lines, SNP alleles and haplotypes in terms of interested phenotypic traits (P<0.05), and also SNP and haplotype distributions changed depending on quail lines (P<0.001). When all results were evaluated together, it was concluded that the fifteen generations of selection caused significant changes in the LEPR gene in terms of economically important traits in Japanese quail lines (C. coturnix japonica).