Isoamyl acetate is an important flavor compound in wine and beverage. It is formed from isoamyl alcohol and acetyl-CoA catalyzed by alcohol acetyltransferase (AATase) in Saccharomyces cerevisiae. In this study, the gene ATF1 coded for AATase from S. cerevisiae BCRC 21731 was cloned and constructed into a constitutive expression vector pGAPZA. A recombinant Pichia pastoris strain was obtained express high level natural flavor to produce isoamyl acetate. The optimal culture condition to enhance the production of isoamyl acetate by recombinant P. pastoris was also investigated. The results showed that recombinant strain GS115/GAPZA-ATF1 produced twice as much isoamyl acetate as GS115/GAPZA (control strain). When glucose, other than glycerol or methanol, was used as carbon source, recombinant strain produced the highest amount of isoamyl acetate. The optimal medium composition for isoamyl acetate production by recombinant strain was 2% glucose, 1% yeast extract and 20 mM isoamyl alcohol. The highest production of isoamyl acetate, is 0.87 mM, was obtained when the recombinant strain GS115/GAPZA-ATF1 was cultivated in the optimal medium at 30℃ for 4 days.