Flesh browning after cutting or bruising reduces the commercial value of apple fruit. Here, we investigated the genetic factors that regulate flesh browning (at 15 min and 24 h after grating) by a genome-wide association study (GWAS) of 24 sib-families (468 genotypes). Three quantitative trait loci (QTLs) were detected on chr5, chr16, and chr17. Their effects were estimated in a germplasm collection of 86 cultivars and selection lines: flesh browning differed with the genotypes of SNPs linked to these QTLs, respectively explaining 31.3%, 3.3%, and 23.7% of phenotypic variance at 15 min, and 36.7%, 11.0%, and 14.8% of variance at 24 h. Homozygous recessive alleles at these QTLs were associated with low browning. 'Aori 27', a rare cultivar that never browns even 5 days after grating, was homozygous recessive at all three QTLs. Browning was clearly lower in cultivars that were homozygous recessive at two QTLs, rather than one or none. We analyzed browning-related traits-polyphenol oxidase (PPO) activity, total polyphenol content, and juice browning-by GWAS using the germplasm collection. A QTL for PPO activity was detected on chr5, where PPO genes are located; and QTLs for total polyphenol content and juice browning were detected on chr16, where leucoanthocyanidin reductase gene is located. No QTLs for the browning-related traits were detected on chr17. These results indicate that the juice browning is mainly regulated by polyphenol content (chr16 QTL), whereas the flesh browning is also regulated by additional factors, including PPO activity (chr5 QTLs). These findings will facilitate development of non-browning apple cultivars.