Studying genomes of O. oeni strains having opposite oenological aptitudes is important for understanding why this lactic acid bacterium involved in malolactic fermentation is so well adapted to wine. Here, the genome of a strain ATCC BAA-1163, is described and compared with the recently reported genome of the better wine-adapted strain PSU-1. The BAA-1163 genome (8X) was obtained by shotgun sequencing and Phrap assembling. Compact and 62% AT-rich, it consists of a circular 1,792,103-bp chromosome and a 3,948-bp plasmid. It was analysed through a CAAT-Box annotation platform and manually inspected. A total of 51 RNA genes were detected, including two rRNA operons (the second resulting from a duplication of the original one) and 43 tRNAs genes scattered throughout the chromosome. A total of 1,756 ORFs were predicted of which 73% were functionally classified, revealing a specialized metabolic repertoire. The genomic distribution, genetic environment and phylogenetic origin of detected pseudogenes and mobile genetic elements (MGEs) were analyzed. The conservation of gene repertoire and genomic organization were investigated through intra- and inter-species genomic comparisons. BAA-1163 genome was 11.6-kb longer than its PSU-1 counterpart, with macroscopic (i.e. a 674-kb chromosomal inversion between the rRNA operons), and microscopic/small-range rearrangements (local gain/loss of genetic objects). The latter event appeared to affect loci of key metabolic functions presumably involved in wine adaptation, all of them sharing unusual GC-content and abundance of MGEs. These results point up the role of horizontal gene tranfert and MGEs in O. oeni genome plasticity, and give us clues of the genetic origin of its oenological aptitudes. A previous draft has already been released, the complete genome will become available to the scientific community later.