Objective To analyze the genetic characterization of VP1 region of Coxsackie virus A10(CVA10)isolated from clinical specimens of hand, foot and mouth disease(HFMD) patients in Shandong Province. Methods Clinical specimens were collected from some of HFMD patients from 2008 to 2009. The virus was isolated by cell culture. Total RNA was extracted, and the VP1 genes of the isolates were amplified by reverse transcription-polymerase chain reaction (RT-PCR) and sequenced. The genotypes were identified by molecular typing method and bioinformatics analysis.Homologous comparison and phylogenetic analysis of representative CVA10 strains were performed.Homologous comparison between the Shandong isolates and strains obtained from GenBank were performed and phylogenetic analysis of some representative CVA10 strains were performed. Results Three hundred and thirty viruses strains were isolated from 760 clinical specimens collected from HFMD patients, and 17 of them were identified as CVA10. The homologies of nucleotide and amino acid of the 17 CVA10 strains were 82.3%-100.0% and 94.2%-100.0%, respectively. Compared with the prototype strain of CVA10 (Kowalik/USA/2003), the homologies of nucleotide and amino acid were 75.6%-76.8% and 90.2%-93.2%, respectively. Interestingly, Shandong CVA10 strains were clustered into two distinct subgroups in the phylogenetic tree. Conclusions CVA10 is one of the causative agents of HFMD. Two independently circulating subgroups of CVA10 exist in Shandong province.