Objective To study the etiological agent of hand, foot and mouth disease ( HFMD) and the genetic characteristics of coxsackievirus A16 ( CVA16 ) strains isolated from clinical specimens of patients with HFMD in Liaocheng city in 2013.Methods Throat swab and stool specimens were collected from patients with HFMD in the disease surveillance hospitals in Liaocheng city from January to December 2013.Samples pos-itive for CVA16 strains were screened out for the isolation of virus strains with rhabdomyosarcoma ( RD) cells and Vero cells.The entire VP1 coding regions of 9 randomly selected CVA16 isolates were amplified and se-quenced.BioEdit and MEGA4 softwares were used for homology analysis.A phylogenetic tree among the 9 CVA16 isolates and 56 CVA16 representative strains of known genotypes and subgenotypes was constructed.Re-sults The results of PCR analysis showed that 747(77.73%) out of 961 specimens were positive for HFMD and among them, 74 samples (9.91%) were positive for EV71 strains, 130(17.40%) were CVA16 strains and 543(72.69%) were other enterovirus strains.The 9 CVA16 strains clustered into the B2b evolution branch of B genotype with the representative strains, sharing 97.7%to 100%homologies in nucleotide sequences and 99.3%to 100%in amino acid sequences.Conclusion Although EV71 and CVA16 strains were identified, other enteric viruses were the predominant pathogens causing HFMD in Liaocheng city in 2013.The CVA16 iso-lates belonged to B2b subgenotype.The pathogen spectrum of HFMD had already changed.It is necessary to strengthen the surveillance for EV71, CVA16 and other enteric viruses and understand their genetic characteriza-tions, which would be of great significance for the prevention and control of HFMD.