To investigate whether there is any phylogenetic evidence to support the hypothesis that swine is the natural host of HEV genotypes 3 and 4, Bayesian analysis of 80 full-length genomic sequences of HEV was performed. The results showed that the strains of genotypes 3 and 4 from swine are paraphyletic with regard to strains of human origin, which are thus phylogenetically nested among the swine strains. Recognition of HEV genotypes 3 and 4 as viruses from swine or swine HEV can provide an evolutionary explanation to the observation of cross-species infection by genotypes 3 and 4 HEV.