During apple (Malus × domestica Borkh.) storage, a loss in fruit firmness can occur. This is frequently associated with mealiness, an undesirable trait. There have been studies, such as phenotypic analyses and transcriptomics, as well as others employing a transgenic approach, focusing on this trait. Certain genetic approaches, such as quantitative trait loci (QTL) approach, however, have not been attempted. In this study, to identify and characterize QTLs controlling flesh mealiness and to investigate their application in apple breeding, we performed classical QTL mapping based on a bi-parental population and a genome-wide association study (GWAS) of mealiness. Phenotypic data for mealiness allowed us to identify two QTLs in the bi-parental family located on linkage group 10. The GWAS discovered significant marker-trait associations on chromosomes 2, 9, and 10. The MdPG1 locus, located on chromosome 10, was identified as the locus with the strongest significance by both QTL mapping and GWAS, suggesting its primary contribution to flesh mealiness. Using a tri-allelic simple sequence repeat marker, Md-PG1_SSR10kd, 10 kb downstream of the MdPG1 coding sequence, we divided apple accessions into six groups based on their genotypes. Among the six groups, the Md-PG1_SSR10kd genotype “2/2” had the least mealy phenotype.