In this study, genetic variation of the fat mass and obesity-associated gene (FTO) was detected by PCR-SSCP and DNA sequencing in 618 individuals from five Chinese indigenous cattle breeds, and their genetic effects on meat quality traits were evaluated.The results showed that a novel single nucleotide polymorphism C1071T was detected in exon 5 and the allelic frequencies for the C and T alleles of the five breeds were 0.666/0.334; 0.583/0.417; 0.631/0.369; 0.653/0.347; 0.689/0.311,respectively.Animals with CT genotype had higher mean values for backfat thickness than those with CC or TT genotypes (P < 0.01).Individuals with CC or CT genotypes had higher Iongissimus muscle area than those with TT genotype (P < 0.05).The FTO gene may be a candidate gene for identifying differences in meat quality traits and therefore could be applied to marker-assisted selection of native Chinese cattle breeds.