Objective To understand the pathogenic molecular characteristics of the latest prevalent Group A Streptococcus (GAS) in a suburban area of Beijing. Methods Throat swab specimens from children suspected of GAS infection in the outpatient setting of a sentinel surveillance hospital in a suburban area of Beijing from January 2023 to June 2025 were collected. GAS strains were detected and cultured. Antimicrobial susceptibility testing on 12 antimicrobial agents were performed, and molecular epidemiological characteristics of GAS strains was further analyzed by whole genome sequencing technique. Results Data of 326 children suspected of GAS infection in outpatient setting were collected. A total of 41 GAS strains were detected and cultured, with a detection rate of 12.58%. The proportions of children with anterior cervical lymph node enlargement, tonsil congestion, and jaw congestion in the GAS positive group were all higher than those in the GAS negative group, and differences were all statistically significant (all P < 0.05). All 41 GAS strains carried both erm (B) and tet (M) resistance genes and exhibited a structural type (cMLS) resistance phenotype. All of the emm12 strains were ST36, and emm1 strains were ST28. A total of 6 emm12 subtypes and 1 emm1 subtype were detected, namely emm12.2, emm12.95, emm12.69, emm12.17, emm12.19, emm12.149, and emm1.12. Among them, emm12.149 was a newly discovered subtype. Nucleobase at the 175 100 locus in gene sequence had undergone an A → T mutation. A total of 5 bacteriophages and 6 superantigens were detected. There were statistically significant differences in multi-nucleotide polymorphisms (MNPs) and insertion numbers in the genomes of emm12.0 and emm12 subtypes (both P < 0.05). The phylogenetic tree presented a highly clonal group of 23 GAS strains in this area, accounting for 57.50%. Conclusion The prevalent GAS strain in this area is emm12. emm12.149 is a new subtype. The resistance genes and phenotypes are erm (B), tet (M), and structural type (cMLS). The genome has plenty genetic polymorphism, and the genome sequences of multiple GAS strains are highly cloned, indicating the possibility of clone transmission. This suggests that the surveillance of GAS in sentinel hospitals should continue to be strengthened, so as to provide theoretical basis for the prevention and control of GAS epidemics.