Streptococcus suis is an important pathogen for both swine and humans. In this study, we genotyped 105 S. suis isolates from porcine endocarditis in East Japan on the basis of profiles of capsular serotype-specific, virulence-associated and pilus-associated genes. The most common genotype was cps2J/mrp+/epf-/sly-/sbp2-/sep1-/sgp1+ (76.19%), followed by nt(non-typeable)/mrp+/epf-/sly-/sbp2-/sep1-/sgp1+ (7.62%) and cps2J/mrp+/epf+/sly+/sbp2+/sep1-/sgp1- (7.62%). The representative isolates of mrp+/epf-/sly-/sbp2-/sep1-/sgp1+ were classified into ST28 complex, a clonal complex previously referred to as ST27 complex, whereas those of mrp+/epf+/sly+/sbp2+/sep1-/sgp1- were classified into ST1 complex by multilocus sequence typing. Because the majority of human clinical isolates were assigned to ST1 and ST28 complexes, most isolates from porcine endocarditis investigated in this study may have the potential to cause S. suis infection in humans.