Objective:To provide useful information for in-depth understanding of the epidemic and molecular evolution of Coxsackievirus A4 (CV-A4), the genetic characteristics of the complete genome and recombination events in some genome regions of CV-A4 strain isolated from a patient with severe hand, foot and mouth disease (HFMD) in Yunnan province were analyzed.Methods:The CV-A4 strain was isolated from feces using RD, KMB17 and A549 cells respectively, and the viral RNA was extracted from the supernatant with CPE. The whole VP1 and complete genome sequences of the virus were amplified by RT-PCR and sequenced through Sanger’s sequencing. Complete genome sequence and genome regions of the isolated virus were analyzed through MEGA7.0 and SimPlot 3.5.1 software.Results:The virus isolated from RD cells belonged to CV-A4 and was designated as R11-20/YN/CHN/2011 strain. This CV-A4 strain was C2 sub-genotype through phylogenetic analysis based on the VP1 sequence. CV-A4 R11-20/YN/CHN/2011 has the highest nucleotide sequence identity with 09214/SD/CHN/2009 in VP1 and CVA4/SZ/CHN/09 in the complete genome. Recombination occurred between CV-A4 R11-20/YN/CHN/2011 and EV-A71 in 3D region.Conclusions:The CV-A4 R11-20/YN/CHN/2011 strain belongs to C2 sub-genotype and recombines with EV-A71 in 3D region.