To understand the genotype distribution and molecular epidemiological characteristics of hepatitis E virus (HEV) isolated in Shandong Province, 2017. The cases of hepatitis E who were reported to the National Notifiable Disease Reporting System (NNDRS) from January to December 2017 in Shandong Province were chosen as the subjects in the study. Epidemiological information and blood samples were collected from 1 045 participants. Both anti-HEV IgM and anti-HEV IgG were detected using ELISA method. Viral nucleic acids were extracted only from those of anti-HEV IgM positive samples. Nested reverse transcription-polymerase chain reaction was carried out to amplify 644 bp nucleotide sequences within HEV open reading frame (ORF) 2 region. The sample sequences together with reference sequences from GenBank were subjected to phylogenetic analysis. In total, 638 (61.1%) cases were detected positive for anti-HEV IgM. The average age of male was (57.9±12.2) years, and the anti-HEV IgM positive rate was 61.5% (496/807). The average age of female was (58.1±15.0) years, and the anti-HEV IgM positive rate was 59.7% (142/238). A total of 163 HEV strains were detected, and the positive rate was 25.6% (163/638). The positive rate of the eastern, central and western region was 23.0% (71/309), 33.6% (72/214) and 17.4% (20/115), respectively. Phylogenetic tree and homology analysis indicated that all isolates belonged to genotype Ⅳ, clustering into four different subgenotype (4a, 4b, 4d and 4h). Subgenotype 4d was predominant, accounting for 85.9% (140 strains), followed by 4b (7.4%, 12 strains), 4a (3.7%, 6 strains) and 4h (3.1%, 5 strains). The 4a, 4b, and 4h subgenotype were mainly detected in the eastern region, accounting for 3/5, 11/12, and 4/6, respectively. The 4d subgenotype was mainly in the middle region, accounting for 50.0% (70/140). The homology analysis showed that the 163 sequences shared 82.7% to 100.0% nucleotide sequence identity with each other. The 140 sequences of HEV 4d strains showed high similarity with swine-origin HEV(KF176351), cattle-origin HEV(KU904278)and sheep-origin HEV(KU904267)isolated in Shandong Province, and the nucleotide homology was 93.1%-98.3%, 92.7%-97.9% and 92.7%-97.9%, respectively. HEV genotype Ⅳ(4d subgenotype) was dominant in Shandong province. A complicated interspecies transmission might be the main source of human HEV infection in Shandong Province, China.