While performing a nationwide survey of hepatitis E virus (HEV) infection among 450 wild boars (Sus scrofa leucomystax) that had been captured in Japan between November 2005 and March 2010, we found 16 boars (3.6%) with ongoing HEV infection: 11 had genotype 3 HEV, four had genotype 4 HEV and the remaining boar was infected with HEV of an unrecognized genotype (designated wbJOY_06). The entire wbJOY_06 genome was sequenced and was found to comprise 7246 nt excluding the poly(A) tail. The wbJOY_06 isolate was highly divergent from known genotype 1-4 HEV isolates derived from humans, swine, wild boars, deer, mongoose and rabbits (n=145) by 22.6-27.7%, rat HEV isolates (n=2) by 46.0-46.2%, and avian HEV isolates (n=5) by 52.5-53.1% over the entire genome. A Simplot analysis revealed no significant recombination between the existing HEV strains of genotypes 1-4. Therefore, we propose that the wbJOY_06 isolate is the first member of a previously unidentified genotype.