Streptococcus pneumoniae can produce a wide breadth of antigenically diverse capsule types, a fact that poses a looming threat to the success of vaccines that target pneumococcal polysaccharide (PS) capsule. Yet, many pneumococcal capsule types remain undiscovered and/or uncharacterized. Prior sequence analysis of pneumococcal capsule synthesis () loci suggested the existence of capsule subtypes among isolates identified as "serotype 36" according to conventional capsule typing methods. We discovered these subtypes represent two antigenically similar but distinguishable pneumococcal capsule serotypes, 36A and 36B. Biochemical analysis of their capsule PS structure reveals that both have the shared repeat unit backbone [→5)-α-d-Gal-(1→1)-d-Rib-ol-(5→P→6)-β-d-ManNAc-(1→4)-β-d-Glc-(1→] with two branching structures. Both serotypes have a β-d-Gal branch to Ribitol. Serotypes 36A and 36B differ by the presence of a α-d-Glc-(1→3)-β-d-ManNAc or α-d-Gal-(1→3)-β-d-ManNAc branch, respectively. Comparison of the phylogenetically distant serogroup 9 and 36  loci, which all encode this distinguishing glycosidic bond, revealed that the incorporation of Glc (in types 9N and 36A) versus Gal (in types 9A, 9V, 9L, and 36B) is associated with the identity of four amino acids in the encoded glycosyltransferase WcjA. Identifying functional determinants of -encoded enzymes and their impact on capsule PS structure is key to improving the resolution and reliability of sequencing-based capsule typing methods and discovering novel capsule variants indistinguishable by conventional serotyping methods.