The outbreak of Streptococcus suis recently in some districts of Sichuan Province in China has caused over 30 deaths and over 200 infections in human beings. In order to study the pathogenicity mechanism and to prevent the bacteria from spreading and infecting human beings and swine, we have annotated and analyzed the genomes of two strains, Streptococcus suis P1/7 and 89-1591 respectively. The whole length of P1/7 is 2.007 Mb,and has 1969 ORFs. In contrast, the partial genome sequence of 89-1591 is 1.98 Mb in length and exists in 177 contigs with 1918 ORFs. Analysis shows that the average lengths of CDSs in two genomes are very close, and the numbers of the homolog ORFs are 1306 between those two strains. Most of the toxicity factors of the two strains are homologeous, but there are still some significant differences between those two strains. For example, among the 11 genes (cps2A-cps2K) encoding for the capsules in P1/7, 4(cps2A, 2B, 2I, 2J) are not detected in strain 89-1591.At the same time, the genes encoding EF and Haemolysin in P1/7 are also not found in strain 89-1591. Besides, the genes related to DNA replication, repair and recombination differ from each other significantly and there also exist certain differences among the surface proteins. Those characteristics indicate that those two strains have evolved their own specific functions to adapt to the different environments and that the pathogenesis of the two strains is different. We have accumulated comprehensive genomics information for future systematic studies of S.sui. Our results are helpful for disease prevention,vaccine development, as well as drug design for S.suis.