To reveal the genomic sequence characteristics of coxsackievirus A16 (CoxA16) strain isolated from patients with hand-foot-mouth disease (HFMD) in Henan province. A total of 406 samples were detected by reverse-transcription polymerase chain reaction (RT-PCR) and cell-culture-based isolation of coxsackievirus A16. The whole genome of CoxA16 isolate was amplified using 10 pairs of primers, the sequences were analyzed and phylogenetic tree was generated by bioinformatics software. The full length of HN1162/HN/CHN/2010 genome was 7411bp. Compared with the other CoxA16 strains released in GenBank, the nucleotide similarities were 87.0-97.9%, 77.0%-95.4%, 80.3%-96.9%, 77.9% 96.2%, 80.5-100% in 5'UTR, P1, P2, P3, 3'UTR region, respectively; The similarities of nucleotide and amino acid sequences in VP1 region were 91.4%-96.4% and 99.3%-99.7%, respectively. Phylogenetic tree analysis showed that CoxA16 strains isolated from Henan, Shenzhen, Guangzhou and Fujian belonged to the same cluster. The newly isolated CoxA16 from Henan province belonged to subgenotype C2/B-2. These results will have great significance in monitoring CoxA16 and for prevention and control of hand-foot-mouth disease.