Emergence of fatal Streptococcus suis serotype 2 (S. suis 2, SS2) in China, 2005, has greatly challenged the public health, raising serious concerns about its global circulation. Whole genome sequencing of the representative strains has identified a potential pathogenicity island (PAI), named 89K. Here, we reported the recurrence of human S. suis meningitis cases (two in Shenzhen City and one in Sichuan Province) in China, in 2007. Multiple lines of evidence supported that these human cases are caused by highly pathogenic SS2 isolates. Pulsed-field gel electrophoresis analysis indicated that these re-emerging SS2 isolates (07CQH01, 07SZH01 and 07SZH02) can be featured with different genotypes. Molecular dissection demonstrated that they all share 89K, the newly proposed PAI that is common to 2005 prevalent strains in China. Further mapping of 89K revealed that gene losses/deletions occur in 07CQH01 and 07SZH01, except 07SZH02. These findings suggested that heterogeneous SS2 circulates in China, with the capability of causing endemic with life-threatening danger.