BACKGROUND: During grapevine domestication somatic variation has been used as a source of diversity for clonal selection. OBJECTIVE: This work provides additional information on the molecular mechanisms responsible for berry skin color reversion on a subset of somatic variants for berry skin color never investigated before. METHODS: The berry color locus and its surrounding genomic regionwere genetically characterized through a layer-specific approach, which has already been proven to be a successful method to decipher the molecular mechanisms responsible for color reversions on somatic variants. RESULTS: Deletions of different extent and positions were detected among less-pigmented/unpigmented variants derived from a pigmented wild-type. These deletions affected only the inner cell layer in the less pigmented variants and both cell layers in the unpigmented variants. Regarding the pigmented variants derived from an unpigmented wild-type, only one group was distinguished by the Gret1 retrotransposon partial excision from the VvMybA1 promoter. Moreover, within this latter group, VvMybA2 showed an important role regarding the phenotypic variation, through the recovery of the functional G allele. CONCLUSIONS: This investigation focused on the berry color locus using somatic variants for berry skin color, promotes a better understanding of the evolutionary events behind their origin and variability, opening an opportunity for their use in the genetic improvement of varieties.