Capsular polysaccharide is an important virulence determinant for the nosocomial pathogen, Acinetobacter baumannii. We have previously shown that the genetic content at the capsule biosynthesis locus (K locus) varies extensively between clinical isolates belonging to the two major clonal lineages, and this is expected to have negative implications for vaccine development and phage therapy. Bioinformatic tools were used to examine proteins encoded by different KL gene clusters found in draft genomes of Australian antibiotic-resistant GC1 isolates. The KL12 gene cluster found in the genome of isolate D36 contains genes predicted to enable the synthesis of simple sugars, as well as genes for N-acetyl-L-fucosamine (L-FucpNAc) and N-acetyl-D-fucosamine (D-FucpNAc) synthesis. It also contains a module of 10 genes, 6 of which are required for synthesis of 5,7-di-N-acetyllegionaminic acid, a non-2-ulosonic acid associated with virulence properties in other bacteria. The remaining four genes were unique. The chemical composition and structure of capsule purified from D36 were determined using Nuclear Magnetic Resonance (NMR). The K12 repeat unit contained N-acetyl-D-galactosamine. It also contained D-FucpNAc and L-FucpNAc confirming bioinformatic predictions. A novel non-2-ulosonic acid, 5,7-di-N-acetylacinetaminic acid (Aci5Ac7Ac), which has never previously been recovered from a biological source, was also found. Aci5Ac7Ac is the 7,8-epimer of Leg5Ac7Ac, and a biosynthetic pathway for Aci5Ac7Ac from Leg5Ac7Ac was proposed. Examination of other genes in KL12 further allowed for the prediction of the first sugar, as well as the role of different proteins in the assembly of the capsule unit in the cytoplasm. The results highlight how capsule sugar compositions and structures can be used to confirm biosynthesis pathways predicted via bioinformatic analysis. Examination of the genetics and chemical structures of these major antigenic structures is the first step towards understanding the role of capsule variation in the success of A. baumannii clones in the hospital environment.