Most enteroviruses excreted in human feces and urine are present in environmental water. In order to clarify the infection route of enterovirus, the detection of viruses in both clinical and environmental samples may contribute to understanding the mode of transmission of strains responsible for human infection. Thus, 21 epidemic enterovirus 71 strains from environmental water or stool samples were collected from HFMD children during 2005. Enterovirus genomic RNA was first amplified directly from clinical and environmental samples and then characterized by DNA sequencing and phylogenetic analysis. Results showed that these clinical strains share similar sequence identity (86.4-86.8%) to prototype BrCr based on the 5'-nontranslated region (NTR). However, environmental strains, except HME 77, share similar sequence identity (86.2-87.2%) to prototype BrCr. HME 77 showed higher sequence identity (90.1%). Results from phylogenetic analysis revealed that five environmental isolates were clustered as genogroup 3, which was closely related to a Taiwan outbreak in 1998 (AY055133). HME 77 was more closely related to a China epidemic isolate (AY895144), which belonged to genogroup 4. In contrast, all strains from clinical samples tested belonged to genogroup 3, which clustered with AY055133. In conclusion, there are two major epidemic clones (genogroups 3 and 4) prevalent in Taiwan since 2004 either in water or clinical patients.