The objective of this study was to determine the probable pathogen causing the recently discovered hepatopancreas browned disease (HPBD) in Chinese mitten crab (Eriocheir sinensis), an important freshwater aquaculture species. Hepatopancreas material was collected from 30 E. sinensis individuals confirmed as infected using plasma coagulase tests. Genes nuc and femA, both specific for Staphylococcus aureus, were amplified by reverse transcription-PCR from three randomly selected HPBD-infected crabs, specific bands were observed at 191 and 397 bp, and amplified partial sequences aligned perfectly (100%) with published nuc and femA gene sequences using BLAST and GenBank. Four major developmental stages of hepatopancreas histopathological changes were observed in 7-week reverse infection challenge tests in 90 pathogen-induced animals; hepatopancreas material changed colour from orange to yellow, red to brown, and light brown to almost fully necrotised. Optical and transmission electron microscopy revealed similar hepatopancreas pathological characteristics to those of HPBD-infected E. sinensis. The hepatopancreas browning rate of infected crabs (88.89 ± 5.09%) was significantly higher than controls (7.78 ± 1.92%). These results suggest S. aureus is the probable pathogen causing HPBD in E. sinensis, and infection leads to inflammation, atrophy, and complication of hepatopancreatic necrosis.