This invention concerns a method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain including the steps of: (a) cultivating a Yarrowia strain, said strain including a deletion among at least three genes, the phenotype associated with each of these deletions corresponding to an auxotrophy or to a dominant character for this strain; (b) transforming said Yarrowia strain thus obtained with at least three recombinant vectors that include selection markers allowing, for this strain, the complementation of auxotrophy and, potentially, of the dominant character resulting from each of these deletions; and (c) selecting, on a minimum medium, the yeasts having integrated said at least three recombinant vectors. This invention also includes a method for producing a polypeptide of interest using this method as well as a method for obtaining a modified Yarrowia strain including a deletion among at least three genes, the phenotype associated with each of these deletions corresponding to an auxotrophy or to a dominant character for this strain.