Abstract: Objective：To investigate the pathogen distribution of hand-foot and mouth disease(HFMD) from 2013 to 2014 in Hangzhou region, and analyze its genetic characteristics. Methods：A total of 1 340 samples from children with HFMD during March 2013 and April 2014 were collected, and RNA in the sample was extracted. Then, the full-length VP1 gene was amplified by reverse transcription polymerase chain reaction(RT-PCR) and sequenced, and the viral genotypes were identified by the Blast. The homology of VP1 gene of Coxsackie virus(CV) A6 and A10 was analyzed and the phyletic evolution tree was constructed. Results：The detection rate of enterovirus(EV) in the children with HFMD was 81.43%(1 090/1 340). Among them, the positive rate of CV-A6 was 41.04%, which became the main pathogen of EV instead of EV-71(14.48%). The positive rate of CV-A10 was listed in the third(8.51%), higher than that of CV-A16(3.81%). The analysis of homology of CV-A6 and CV-A10 showed that the nucleotide homology among 25 strains of CV-A6 and among 15 strains of CV-A10 were 89.0% 99.7% and 95.3% 99.9%, respectively. The phyletic evolution analysis showed that the main genotypes were G and H for CV-A6 and F and G for CV-A10. Conclusion：The main pathogens of the children with HFMD from 2013 to 2014 in Hangzhou region have changed. CV-A6 is the main pathogen, and CV-A10 also has a potential threat on children. Therefore, it is necessary to continuously monitor and analyze the molecular characteristics of EV.