Objective To analyze the mol. epidemic characteristics of hand, foot and mouth disease(HFMD) in Guangdong and Jiangsu Provinces, China from 2018 to 2019 and provide a basis for prevention and control of HFMD and vaccine development. Methods The throat and anal swabs were collected from the patients with HFMD monitored in five clin. centers in Guangdong and Jiangsu Provinces from 2018 to 2019. Samples with pos. results tested by real-time fluorescent quant. PCR were amplified with EV pan primers and specific primers to obtain 5′ UTR region and VP1 region sequences. The pathogen genotypes were determined by BLAST, and phylogenetic trees were constructed based on the VP1 sequences to analyze the mol. epidemic characteristics of main pathogens. Results Of the cases of HFMD in Guangdong and Jiangsu from 2018 to 2019, more than 96% were pos. for CV-A16(63. 69% ∼ 72. 43%)and CVA6(24. 81% ∼ 32. 38%), followed by those for CV-A10 and EV-A71. The EV strains detected in this study were of subgenotypes EV-A71 C4, CV-A16 B1/B2, CV-A6 D3 and CV-A10 F3, which were also the main subgenotypes of HFMD pathogens in mainland China during the past decade. Conclusion CV-A16 and CV-A6 infections caused a relatively large proportion of HFMD cases, which threatened the health of infants and young children. Multivalent HFMD vaccines containing CV-A16 and CV-A6 should be developed.