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The objective of this study was to explore the utility of the phenolic pattern (1) to differentiate or associate between cultivars with a different or same genetic background respectively and (2) to assess some important quality traits (color, disease resistance, and browning) in apple fruit. A unique set of cultivars/candivars occurring in Belgium were selected for this survey. It was possible to segregate the studied apple cultivars/candivars into three clusters: red-flesh apple candivars, classic/new cultivars and candivars and heritage apple cultivars. It was found that the heritage apple varieties selected for their disease resistance and cultivated under organic agricultural practice demonstrate a remarkable different phenolic profile. Furthermore, it was found that the phenolic makeup of the peel could suggest the genetic relationships among the apple cultivars. In conclusion, the knowledge of the phenolic profile could be a useful instrument in breeding programs to identify apples with better quality traits, processing characteristics and health-benefiting effects.