Objective To investigate the relationship between emm typing, regional and virulence gene distribution of group A Streptococcus (GAS) isolated from children with scarlet fever. Methods Specimens from children with scarlet fever in Beijing and Shanghai were collected for GAS isolation and identification, emm genotype and carrying status of 13 kinds of virulence genes (speA, speB, speC, speF, speG, speH, speI, speJ, speK, speL, speM, ssa and smeZ) were detected by polymerase chain reaction (PCR), relationship between distribution of virulence gene and region as well as emm genotype of GAS strains was analyzed. Results Among 114 GAS strains, 60 were emm1.0 and 54 were emm12.0; 52 strains were isolated from Beijing(31 strains were emm1.0 and 21 were emm12.0), and 62 strains were from Shanghai(29 were emm1.0 and 33 were emm12.0). The carrying rates of speA, speC, speG, speH, speI, speJ, speK, ssa and smeZ were 52.6%, 76.3%, 80.7%, 43.9%, 55.3%, 57.0%, 75.4%, 97.4%, and 93.0% respectively, carrying rates of speB and speF were both 98.2%, speL and speM genes were not found. There were significant difference in carrying rates of speA, speH, speI and speJ genes of emm1.0 and emm12.0 GAS strains in Beijing as well as speA, speH, speI, speJ and speK genes of emm1.0 and emm12.0 GAS in Shanghai (all P < 0.05). Carrying rates of speC, speH, speJ and speK of emm1.0 GAS strain, as well as carrying rates of speC, speH, speI, speJ and speK of emm12.0 strain between Beijing and Shanghai were all significant (all P < 0.05). Conclusion Distribution of virulence genes of GAS strains is different with emm genotyping and region.