The genus of the Acetobacter is industrially important for the production of vinegar and beverages, due to their ability to oxidize different kind of sugars and alcohols. Current taxonomy in the Acetobacter genus comprises of 22 species, and these are phylogenetically divided into two groups (Acetobacter aceti and Acetobacter pasteurianus group) [1]. The Acetobacter strains have been considered as the spoilage bacteria, such as acetification, ropiness, turbidity, off-flavors and discoloration in beer, and rot in apples, pears and pink disease in pineapples [2,3]. Comparative analysis of the 16S rRNA gene sequence is a commonly used molecular method for bacterial taxonomy and identification [4]. Strains that generally show 97% sequence similarity in the 16S rRNA genes are considered to be the same species [5]. Unfortunately, high degrees of similarity (reaching 95.7e99.8% and 97.0e99.9%) have been observed for the 16S rRNA gene sequences among the A. aceti and A. pasteurianus group. The tuf gene sequences have been widely used as a putative species DNA marker for phylogenetic analysis in a variety of lactic acid bacteria (LAB) [6,7], and Enterobacterial species [8]. The tuf gene has been used as the target for detection and identification of several species of bacteria based on the PCR assay [9e12]. Therefore, we analyzed partial tuf gene sequences and compared them to that of the 16S rRNA gene to evaluate the utility of tuf as an alternative marker for discriminating Acetobacter strains. Moreover,