Abstract: Analyzing the genomic changes of microorganisms at molecular level and genetically modifying them to increase the yield of pullulans polysaccharides is currently an urgent problem to be solved. The genome of a high-yield pullulans producing strain(TN-31) was compared with other strains of Aureobasidium spp. by using the comparative genomics method. The results showed that this strain had undergone genome duplication, and a large amount of genetic variations was presented in its genome, which might be the reason for the high-yield production of pullulans. In addition, the genome size of this strain was higher than that of any other Aureobasidium strains, and the special regulatory sequences of its unique and functional gene promoter regions might enable it be different from other strains of Aureobasidium spp.. This special phenotype was possibly due to strain-level adaptive evolution, which ensured this strain adapt to the harsh environment through genetic variation and adaptive selection.