Abstract: Objective To understand the etiological characteristics of pathogens of hand foot and mouth disease (HFMD) and the molecular epidemiological characteristics of Enterovirus 71 (EV71) and Coxasckievirus A16 (Cox A16) in Tianjin in 2010. Methods Clinical specimens from HFMD patients were detected by using Real-time PCR. EV71 and Cox A16 strains were isolated from some positive specimens by using RD cell. VP1 genes of the isolates were amplified by using RT-PCR. Sequencing and phylogenetic analysis were carried out with biology software. Results A total of 1766 specimens were detected, the overall positive rate of enterovirus was 71.52%(1263/1766). EV71 accounted for 43.94% and Cox A16 accounted for 41.65% of the total positive specimens, other enterovirus only accounted for 14.41%. Fifteen EV71 isolates had the highest homology with the representative strain of C4a cluster of the C4 subtype, 9 Cox A16 isolates had the highest homology with the representative strain of B1 subtype, in which 8 belonged to B1b cluster, 1 belonged to B1a cluster. Conclusion C4a strain of EV71 and B1b strain of Cox A16 were the major pathogens to cause HFMD in Tianjin in 2010.