Aims: To investigate the presence of enterovirus RNA in various samples of environmental water collected in Taiwan during 2004-2005, and to characterize the genotypes and distribution of the viruses identified in Taiwan. Methods and Results: Total 131 environmental samples were screened using the reverse transcription polymerase chain reaction (RT-PCR) for the highly conserved 5'-nontranslated regions (5'-NTR). Among these enterovirus RNA-positive samples, 32, 15 and 6 of the samples were recovered from surface water, ground water and sewage water respectively. However, the total positive detection rate increased to 40.5% with the application of seminested PCR. Sequencing revealed that the majority of isolates belonged to the following genotypes: coxsackie A2 (35.8%), coxsackie A6 (13.2%) and enterovirus (EV)71 (11.3%); echovirus 11, porcine EV9 and coxsackie A16 isolates were also observed. Conclusions: This study confirms that the major epidemic genotypes of enterovirus are prevalent in the surface and ground water of Taiwan. Significance and Impact of the Study: This study is helpful in understanding the significance and epidemiology of the virus within and beyond the study area. Moreover, it was possible to predict the enterovirus genotype and evaluate possible correlations between water contamination and viral sequences found among clinical samples.