The seaweed, Gelidium amansii, was fermented to produce bioethanol. Optimal pretreatment condition was determined as 94 mM H2SO4 and 10% (w/v) seaweed slurry at 121°C for 60 min. The mono sugars of 43.5 g/L with 57.4% of conversion from total carbohydrate of 75.8 g/L with G. amansii slurry 100g dcw/L were obtained by thermal acid hydrolysis pretreatment and enzymatic saccharification. G. amansii hydrolysate was used as the substrate for ethanol production by separate hydrolysis and fermentation (SHF). The ethanol concentration of 20.5 g/L was produced by Scheffersomyces stipitis KCTC 7228. The effect of HMF on ethanol production by S. stipitis KCTC 7228 was evaluated and 5-hydroxymethylfurfural (HMF) was converted to 2,5-bis-hydroxymethylfuran. The accumulated 2,5-bis-hydroxymethylfuran in the medium did not affect galactose and glucose uptakes and ethanol production. Biotransformation of HMF to less inhibitory compounds by S. stipitis KCTC 7228 could enhance overall fermentation yields of seaweed hydrolysates to ethanol.