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Over 500 microorganisms isolated from Korean traditional foods, Maeju (source of soybean paste) and Nuruk (Korean koji), were screened to obtain an isomaltulose-producing microorganism. It was identified as Enterobacter sp. FMB-1 by 16S rRNA sequencing and the API 20E system. It had a greater than 90% conversion of sucrose (as 4 g/l) to isomaltulose in 2 days. Small amounts of trehalulose, glucose, and fructose were produced as byproducts, implying that this strain could be possibly employed in the production of isomaltulose in industry.