Understanding the factors that limit recombination in bacteria is critical in order to better understand and assess its effects on genetic variation and bacterial population genetic structure. Transformation in the naturally competent bacterium, Streptococcus pneumoniae, is regulated by a polymorphic competence (com) apparatus. It has been suggested that polymorphic types, called pherotypes, generate and maintain subpopulation genetic structure within this species. We test predictions stemming from this hypothesis using a cosmopolitan sample of clinical pneumococcal isolates. We sequenced the locus encoding the peptide that induces competence (comC) to assign clones to each known pherotype class and then used multilocus sequence typing to determine whether there is significant genetic differentiation between pherotypes subgroups. We find two dominant pherotypes within our sample, and both are maintained at high frequencies (CSP1 74%, CSP2 26%). Our analyses fail to detect significant genetic differentiation between pherotype groups and find strong evidence, from a coalescent analysis, for interpherotype recombination. In addition, our analyses indicate that positive selection may account for the maintenance of the fixed polymorphism in this locus (comC). Altogether, these results fail to support the prediction that the polymorphism in the competence system acts to limit recombination within S. pneumoniae populations. We discuss why this result is expected given the mechanism underlying transformation and outline a scenario to explain the evolution of polymorphism in the competence system.