In August 2018, an infectious disease with high mortality and hemorrhagic symptom occurred in Acipenser baerii in Pengzhou and Qionglai Counties, Sichuan Province, China. Bacterial examination, PCR detection of acipenserid herpesvirus 2 (AciHV-2) and pathological examination of liver and kidney of A. baerii were performed to elucidate the aetiology. Two strains of gram-positives chain-forming cocci were isolated from the diseased A.baerii, and the 16S rRNA gene sequencing analysis by BLAST in GenBank indicated that the two isolates (MN416231 and MN416230) showed a high level of similarity to Streptococcus iniae (more than 99%). A phylogenetic tree based on the 16S rRNA sequences indicated that the two isolates and other S. iniae strains were grouped into a same branch. In addition, specific PCR detection for lctO gene of S. iniae showed that the two isolates were positive. Based on the 16S rRNA gene sequencing analysis and specific PCR detection, two isolates were identified as S. iniae. The total DNA was extracted from liver and kidney tissues of diseased A. baerii for PCR detection of AciHV-2 polymerase gene, and a 501 bp target band was amplified. A phylogenetic tree based on the sequences indicated that the two samples(QL2, PZ2)and other AciHV-2 strains were clustered together in a branch. Histopathologically, degeneration, necrosis, hemorrhage and infiltration of the inflammation cells occurred in multiple tissues and organs, particularly obvious in liver, kidney, gill, spleen and intestine. A large number of cells invaded by herpesvirus-like particles with a diameter of 200-220 nm and streptococcus with a diameter of 0.7-0.8 microns were observed using electron microscopy, which caused cell damage. In conclusion, the etiology of the diseased A. baerii was a co-infection of S. iniae and AciHV-2.