Aureobasidium pullulans Y2311-1 is a yeast-like fungus that can produce poly(β-L-malic acid). Here, we report the draft whole-genome sequence of the A. pullulans Y2311-1 strain, which includes 14 scaffolds (ranging in size from 0.02 to 3.52 Mb, 25.41 Mb total, 50.09% GC).