Recently, 2 serologically and biochemically distinct subtypes-11Aα and 11Aβ-were discovered among serotype 11A isolates of Streptococcus pneumoniae. Sequence comparison of the capsular polysaccharide synthesis (cps) loci of the 2 subtypes identified disruption of the wcjE gene, a putative O-acetyltransferase, as the genetic hallmark of the 11 Aβ phenotype. Directed disruption of wcjE in vitro in an 11Aα strain switched the strain to the 11Aβ phenotype, confirming the role played by the gene in the divergence between the subtypes. Furthermore, sequences from 7 11Aβ clinical strains each contained unrelated disruptive mutations in the wcjE gene, displaying an unprecedented degree of genetic heterogeneity in a pneumococcal serotype. We propose to name the 11Aα subtype as serotype 11A and the 11Aβ subtype as 11E, a new serotype. Our findings also suggest that the diversity of pneumococcal capsules is much greater than was previously recognized. © 2010 by the Infectious Diseases Society of America. All rights reserved.