Objective:To understand the genome-wide sequence variation and molecular evolution of coxsackievirus A4 (CV-A4) strain in Anhui province, so as to provide a theoretical basis for the pathogenic monitoring and scientific prevention and treatment of hand, foot and mouth disease in the future.Methods:Five CVA4 isolates of 2020 were sequenced by first-generation sequencing method. MEGA11.0 was used to construct a phylogenetic tree based on VP1 region for 5 CV-A4 isolates, 32 CV-A4 strains and Enterovirus A71(EV-A71) prototype strain BrCr, and the isolates and enterovirus A (EV-A) prototype strains based on P1, P2 and P3 regions respectively, and DNAStar was used for amino acid sequence comparison in VP1 region. BioEdit7.2 was used for amino acid displacement entropy analysis and amino acid site entropy mapping. SimPlot3.5 and RDP4 were used for recombination analysis of CV-A4 isolate and EV-A prototype representative strains, and DnaSP6 software was used for selection pressure analysis of isolates and reference representative strains.Results:The phylogenetic tree showed that the isolates belonged to the C2 subtype, which belonged to the same clade as the CV-A4 strain circulating in Chinese mainland, and the amino acid sequence homology of the C2 subtype branch was 97.3%-100%, and the isolates had 6 amino acid variation sites compared with the prototype. The selection pressure analysis showed that the CV-A4 strain of the C2 subtype was affected by negative selection pressure, and there were 25 mutagenic sites in the amino acid sequence in the coding region of the displacement entropy analysis, accounting for 1.14%, and the evolution of the strain mainly depended on recombination. Recombination analysis showed that the isolates recombined with a variety of EV-A prototype strains in the P2 and P3 regions, and the recombination section with the CV-A5 prototype strain was longer, especially in the 3A-3C section, and P1 was a relatively conserved region.Conclusions:CV-A4 has frequent recombination events with other EV-A prototype strains in P2 and P3, and the molecular evolution of CV-A4 in Anhui should continue to be closely monitored.