Since May 2015, severe outbreaks of hepatitis-hydropericardium syndrome (HHS) associated with infections of fowl aviadenovirus (FAdV) have emerged in broiler chickens in several Chinese provinces. To identify the genotype and gain a better understanding of the genetic properties of the FAdV strains responsible for the recent HHS outbreaks in China, the complete genome sequences of five isolates from outbreaks of HHS in broiler chickens in five provinces were determined. The results demonstrated that a novel fowl aviadenovirus 4 (FAdV-4) genotype was epidemic in China. To investigate the molecular characteristics of these Chinese FAdV-4 isolates, their genome contents were compared with those of reported pathogenic and non-pathogenic FAdV-4 strains. The comparative analysis revealed that the novel Chinese FAdV-4 isolates contain various genomic deletions and multiple distinct amino-acid mutations in their major structural genes. Two additional putative genetic virulence markers in the fiber 2 gene were identified. These findings confirmed some of the genetic differences between the pathogenic and non-pathogenic FAdV-4 isolates. The data presented in this report will enhance the current understanding of the molecular epidemiology and genetic diversity of FAdV-4 isolates in China and will provide additional insight into the critical factors that determine the pathogenicity of FAdV-4 strains. Finally, the emergence of this novel and highly pathogenic FAdV-4 genotype emphasizes that preventive measures against FAdV-4 infections on poultry farms should be implemented in China.