<p><b>OBJECTIVE</b>To analyze the genetic evolution for the common causative agent of hand, foot and mouth disease(HFMD) that VP4 of human enterovirus 71 in Shenzhen district.</p><p><b>METHOD</b>491 sttol specimen were collected from, children with hand, foot and mouth diease in Shenzhen Children's Hospital 2009. After cell culture, VP4 gene of eight EV71 strains were amplified by reverse-transcriptase PCR( RT-PCR), phylogenetic analysis of the VP4 gene was constructed by using MEGA 4. 0.</p><p><b>RESULT</b>The VP4 gene of eight EV71 strains encoding 69 amino acids with full length 207 bp. The nucleotide homology of VP4 gene among eight EV71 strains was 94. 2% -98. 1%, compared with VP4 gene of EV71 strains retrieved from Shenzhen 2001 to 2004 and GenBank was 89. 1%-98. 1% and 79.2%-100% respectively. Asian epidemic strain Fuyang had the highest nucleotide homology, representative strain C4 and Shenzhen strain (AY895144) with 94. 2% -98. 1% secondly. Except for the 54th amino acid of VP4 gene of India reported strain and one of the eight EV71 strains, the homology of the rest amino acids between the eight EV71 strains and those in GenBank was 100%. Compared with representative strain C4,there were seventeen differences in nucleotide sequences of VP4 of the eight EV71 strains. All of the different nucleotides were located at the degenerate password sites except one. There was no significant difference in VP4 gene between the severe and the mild cases of strainS. The eight Shenzhen EV71 strains were classified as sub-genotype C4 in the phylogenetic tree.</p><p><b>CONCLUSIONS</b>The epidemic of EV71 in Shenzhen 2009 was sub-genotype C4. VP4 gene of EV71 was very conservative which dose not belong to the variation section. The variation of most of nucleotide was invalid variation. The amino acids encoded by VP4 gene which variation was almost zero.</p>