Streptococcus pyogenes are highly prevalent bacterial pathogens, especially in school-aged children. However, the characteristics of asymptomatic carriers vary geographically in different countries. We aimed to investigate S. pyogenes isolated from healthy schoolchildren in China. From 2007 to 2008, a total of 94 S. pyogenes isolates were obtained from healthy schoolchildren in Beijing and Chongqing, China. Antimicrobial susceptibility testing, determination of macrolide resistance genes (ermB, ermA and mefA), emm genotyping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) were performed. The resistance rate to macrolides was 96.8% and to tetracycline was 92.6%. All macrolide-resistant isolates exhibited constitutive resistance, 77 isolates (84.6%) had the ermB gene, while 14 isolates (15.4%) had the ermA gene. Among the macrolide-resistant isolates, the most frequent emm type was emm12 (51.6%), followed by emm22 (14.3%,) and ST1815 (8.8%). PFGE analysis revealed 12 different patterns, with a given pattern having the same sequence type (ST) by MLST and the same emm type. In conclusion, the rate of macrolide resistance to S. pyogenes is currently very high in China. This is due primarily to the dissemination of a limited number of clones.