The present paper aims to analyze the pathogenic spectrum and molecular epidemiology characteristics of 440 hand, foot and mouth disease（HFMD） cases from partial area of Shanghai in 2010, and to provide a basis for preventing and controlling HFMD in Shanghai. Throat swabs，stool samples and cerebrospinal fluid were collected from 440 HFMD cases. To detect and analyze the etiological agents involved in HFMD, reverse transcriptase-polymerase chain reaction（RT-PCR）, DNA sequencing and phylogenetic tree analysis were performed. Enterovirus 71 (EV71) was detected most frequently, followed by coxsackievirus A16 (CA16), CA6 and CA10. The peak of detection rate of EV71 and CA16 appeared during the summer（May to August）. However, the detection frequency of CA6 and CA10 changed along with the seasons, and reached the peak in winter. VP1 gene sequence analysis of these viruses showed that all EV71 strains belonged to C4a subtype, and highly homologous to the domestic epidemic strains circulating in China recent years. The sequences of 10 Shanghai CA6 strains in this study had a high degree of nucleotide homology (more than 96%) with those strains leading to HFMD outbreak in Finland in 2008, while the phylogenetic tree based on CA10 sequences showed that there were close relationships among Shanghai strains, 2009 Shandong strains and 2010 Yunnan strains, all of which distributed in Asian evolutionary lineage.The study suggested that monitoring on the non-EV71 and non-CA16 enteroviruses which also cause HFMD should be strengthened, and further research on CA6 and CA10 should be carried out to prevent them from spreading quickly.