This dataset contains SNP data obtained by using the Axiom®Apple480K array (Bianco et al., 2016) on 1355 apple accessions from nine mostly European institutions and 92 apple progeny individuals from two parental combinations. Among the accessions, 1341 are diploid, 12 are triploid, and two are doubled haploid. These data were mainly obtained in the frame of the EU seventh Framework Programme project FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/). These data were used in genome-wide association studies by Urrestarazu et al (2017) and Coupel-Ledru et al (2022). This dataset largely overlaps with the dataset “FruitBreedomics apple high-density SNP genotyping dataset” (doi:10.15454/IOPGYF) published earlier. Although released later, the present dataset was generated chronologically earlier than the other dataset with less pedigree-based verification of the Mendelian inheritance consistency of these 275K SNPs. The files with the suffix ".bed" are genotyping matrix in plink binary format, the files with the suffix ".bim" contain positions of loci in plink binary format and the files with the suffix ".fam" contain identifiers of the genotypes plink binary format. This format is described at http://zzz.bwh.harvard.edu/plink/data.shtml#bed.