Sweet cherry germplasm contains a high variety of phenotypes which are associated with fruit size and shape as well as sugar content, etc. High phenotypic variation can be a result of genetic or epigenetic diversity that may interact through time. Recent studies have provided evidence that besides allelic variation, epiallelic variation can establish new heritable phenotypes. Herein we conducted a genetic and an epigenetic study (using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) markers, respectively), accompanied by phenotypic traits correlation analysis in sweet cherry gene pools. The mean genetic diversity was greater than the epigenetic diversity (hgen = 0.193; hepi = 0.185), while no significant relationship was found between genetic and epigenetic distance according to a Mantel test. Furthermore, according to correlation analyses our results provided evidence that epigenetic diversity in predefined populations of sweet cherry had a stronger impact on phenotypic traits than their rich genetic diversity.