Information on hepatitis E virus (HEV) strains circulating in animal reservoirs in Bulgaria is currently lacking. Herein, by screening HEV seropositive sera obtained from Bulgarian swine and wild boars, viral RNA was detected at high prevalence rate (28.2%) in industrial pigs. Sequence analysis of the partial polymerase (RdRp) region revealed the highest genetic correlation with HEVs of genotype (Gt) 3 identified in French and Dutch patients. For three such strains, a 700-bp fragment of the open reading frame 2 gene was generated. On phylogenetic analysis, the Bulgarian strains clustered tightly (93.8–98.3% nt) with human and animal HEVs classified within the Gt3 subtype c.