It has been well known that different strains of Aureobasidium spp. can produce commercial pullulan， polymalate， liamocin， intracellular lipids， gluconic acid， siderophore， melanin and various enzymes. In order to fully elucidate their synthetic pathways and regulation， it is necessary to have an efficient gene editing system for genetic modification of Aureobasidium spp. In this study， an efficient Cre/loxp site-specific recombination system (pAMGDloxp-1， pAMEXlox-1 and pAMCRE1) was constructed. It was found that they could be successfully used to sequentially delete and express many genes in different strains of A.?melanogenum. After each round of gene disruption and expression， over 0.5 positive cells per 1000 competent cells and over 49.8 positive transformants per 1.0?μg DNA were achieved. After each round of the antibiotics gene excision by using the Cre-loxp site-specific recombination， over 95.4?% of the antibiotics-resistant cells became sensitive to both hygromycin B and nourseothricin again. This demonstrated that the Cre/loxp site-specific recombination system constructed in this study can efficiently be used to simultaneously delete and express many genes in different strains of A.?melanogenum. These systems are promising approaches for the easily modifying genomics of the yeast-like fungal strains with enhanced metabolic pathways through multicopy gene deletion and expression.