It has been suggested that S. pneumoniae occur endemically in this area. Since live bacteria could not be isolated from the wild chimpanzees, we have used DNA samples from three apes covering both STs to investigate the capsular type of the S. pneumoniae clones. Recently, a multiplex PCR scheme has been developed to differentiate 29 serotypes most common in the US. The results document the presence of genes involved in CPS of type 3 in all samples. Comparison with known sequences of the cps3 locus from human isolates revealed major differences. Transformation experiments were performed using the laboratory strain R6 as recipient to verify their function. The presence of the S. pneumoniae specific cps3 cluster in samples from dead wild apes confirmed the presence of pneumococci in the deceased animals. The samples investigated here represent both clones that were identified previously STs 2308 and 2309, and were taken seven years apart. Although the allelic profile of the two clones is completely distinct, they contained identical DNA sequences of the cps3 cluster that differed largely from that of other type 3 isolates. It is also remarkable, that among the over 6300 STs listed in the MLST data base in April 2011, no human isolate has the same ST compared to that of the chimpanzee associated S. pneumoniae but differs in at least four out of the seven alleles used for MLST. Several distinct STs for type 3 isolates are known, with ST458 predominating in South Africa, whereas ST180 is the dominant clone in many other countries. The unique cps3Taı¨ sequence adds further evidence that the two clones in the Taı¨ National Park occur endemically, and suggests some selective advantage favouring recent acquisition of this CPS type. Serotype 3 is among the serotypes with the highest invasive capacity in human, and it is thus likely that S. pneumoniae played a substantial role in causing the death of the chimpanzees even though other pathogens have probably contributed to the disease. The capsule is one of the major virulence factors of S. pneumoniae. Clones associated with animals held in captivity or as pets expressed many different serotypes, and most clones were identical to human isolates. However, guinea pigs seemed to be infected by a new clone of serotype 19F, and new clones of serotype 3 were isolated from racing horses. The identification of serotype 3 clones in wild animals described in the present manuscript is another example WZ8040 suggesting that specialized S. pneumoniae clones can be associated with animals. It has been suggested that the animal host of the Taı¨ clones is not the chimpanzee but small rodents or monkeys that are part of the ape’s diet. The reason for the persistence of the S. pneumoniae clones in the Taı¨ National Park is not clear. We do not believe that the capsule itself is involved in this property, since there is no indication that the capsule of the Taı¨ samples is biochemically distinct from the known type 3 structure. It is more likely that other genomic components of these pneumococcal clones are responsible for their capacity to persist in this area.