The hepatitis E virus (HEV) is a leading causative agent of acute hepatitis in humans. Zoonotic HEV strains have been isolated from several animal species, including pigs. New HEV variants have been recently isolated from camels in the Middle East. In the present study, fecal samples from fallow deer, formosan deer, alpaca, and guanaco were analyzed for the detection of HEV. One HEV strain was detected from guanaco, a species of camelids. The nucleotide sequence of guanaco HEV was identical to those of deer HEV-3 strains, which implied the cross-species transmission of HEV-3 from deer to guanaco.