Overexpression of the optimized Vitreoscilla hemoglobin (VHb) gene and the native flavohemoglobin (FHb) gene in Aureobasidium melanogenum P16 rendered a V6 strain and a F44 strain to overproduce pullulan compared to that produced by their wild type strain P16. The capacity to bind CO and oxygen in the V6 strain and the F44 strain was also obviously enhanced. At the same time, the transcriptional levels of the relevant genes were also increased in the V6 strain and the F44 strain and the fused vgbop + the gene encoding GFP and FHb gene + the gene encoding GFP were also actively expressed. During a 10-liter fermentation, the P16 strain produced only 72.0 ± 1.0 g/L pullulan, the yield was 0.77 g/g of sucrose, the productivity was 0.5 ± 0.01 g/L/h and only 79.4% of the total sugar was used. In contrast, the strain V6 yielded 102.3 ± 1.8 g/L of pullulan, the yield was 0.89 g/g of sucrose, the productivity was 0.7 ± 0.01 g/L/h and 96.0% of total sugar was used while 101.4 ± 2.9 g/L of pullulan was accumulated in the culture of the strain F44, the yield was 0.88 g/g of sucrose, the productivity was 0.7 ± 0.02 g/L/h and 96.4% of total sugar was utilized. These data strongly demonstrated that the concentration of pullulan, yield, productivity and sugar utilization were greatly enhanced by overexpression of the VHb and FHb. But their cell growth was almost the similar. •The optimized vgbop gene and the native FHb gene were overexpressed.•Pullulan and the capacity to bind CO and oxygen were greatly enhanced.•The pullulan concentrations, productivity and sugar utilization were also greatly enhanced.