A major limitation of most industrially importantSaccharomyces yeast strains are their inability to efficiently convert starch-rich substrates into commercially important commodities, such as bioethanol, low carbohydrate beer and grain whiskey. In an attempt to overcome this impediment, we have previously expressed inSaccharomyces cerevisiae theLKA1 α-amylase-encoding gene from an efficient raw-starch degrading yeast,Lipomyces kononenkoae. Although the engineeredS. cerevisiae strain was capable of utilising starch, the growth rate was much slower than in glucose-containing media and the ethanol yield in batch fermentations was nowhere near the levels required for an economically, viable bioconversion process. The purpose of the present study was to further improve the fermentation performance of the engineered yeast by expressing theLKA1 gene in a flocculent and non-flocculent genetic background. Despite producing similar levels of α-amylase activities in the extracellular culture media, the flocculentS. cerevisiae transformants degraded starch at an earlier hydrolytic window than the non-flocculent transformants. In small-scale batch fermentations, the non-flocculent strain consumed 76% of the starch supplied in the culture medium and produced 4.61 g l−1 of ethanol after 90 h, while the flocculent strain utilised 82% of the starch and produced 5.1 g l−1 of ethanol after 90 h. Flow-cell system and atomic force microscopy revealed that the ‘tighter’ interaction between the flocculent cells and the starch granules might contribute to the better performance of the flocculent transformant.