Flavin monooxygenase 3 (FMO3) is one member of flavin monooxygenase, FMO3 gene mutation has been proved the main causes of trimethylamine urine of human as well as fishlike smell of milk and eggs. In this study, polymorphism of FMO3 genes in Beijing white quail, China yellow quail and Korean quail was tested by PCR technology and hybrid DNA pool sequencing technology. Results can provide references for further exploring the action mechanism of FMO3 on fishlike smell of quail eggs. Research results show that, One SNPs mutation site (A66G) was detected from the exon 2 of FMO3, the A allele frequencies of A66G in Beijing white quail, China yellow quail and Korean quail were 0.603, 0.500 and 0.574, while G allele frequencies were 0.397, 0.500 and 0.426, respectively. One SNPs mutation site (C219T) was detected from the exon 9, C allele frequencies of C219T in Beijing white quail, China yellow quail and Korean quail were 0.125, 0.250 and 0.000, and the T allele frequencies were 0.875, 0.750 and 1.000, respectively. Two SNPs mutation sites (A39G and A41T) were detected from exon 7, A and G allele frequencies of A39G in Korean quail, Beijing white quail and China yellow quail were 0.811, 0.189, 0.605, 0.395, 0.491 and 0.509, A and T allele frequencies of A41T were 0.000, 1.000, 0.167, 0.833, 0.000 and 1.000, respectively. Two SNPs mutation sites (A139T and C187T) were detected from exon 4, A and T allele frequencies of A139T in Beijing white quail and Korean quail were 0.826, 0.174, 0.351 and 0.649, respectively, C and T allele frequencies of C187T were 0.370, 0.630, 0.283 and 0.717, respectively. According to clustering analysis, Beijing white quail has the closest genetic relationship with Japan quail, partridge, and mallard, which are clustered in one group.