Streptococcus suis (S. suis) has been well-recognized as a zoonotic pathogen worldwide gearing up a great risk to the public health. In this study, an S. suis LSM178 strain with serotype 2 and novel multi-locus sequence type of 1005, isolating from a patient, was interpreted for the pathogenicity by its genetic information. LSM178 was more efficiently invasive to Caco-2 cells than SC19 and P1/7. Phylogenetic analysis showed that LSM178 clustered with highly virulent strains including all human strains and epidemic strains. These serotype 2 S. suis from China shared exclusively the typical virulence characteristics including the maximum (95/96) virulent factors and type I-89 K Pathogenicity Island. Further, groups of genes were identified to distinguish these highly virulent strains from other generally virulent strains, emphasizing the key roles of genes modeling transcription, cell barrier, replication, recombination and repair on the high pathogenicity for highly virulent strains. Additionally, LSM178 contains a novel prophage conducive potentially to pathogenicity. These characters would contribute to deeply studying the pathogenic mechanism and virulence drift of human pathogenic S. suis.