In August 2019, massive mortalities of cultured Hyriopsis cumingii occurred in a local shellfish breeding experimental base in Chongqing, China. In this report, we identified 14 isolates from cultured mussels in mortality events and demonstrated that these strains caused mortality from 9% to 97%. Significant mussel mortality (p < .05) was observed in association with most isolates after bacterial challenge; however, considerable variation in the virulence of different isolates was noted, with survival ranging from 3% to 88% after 7 days. The most virulent strains (HOP3 and GL1) in haemolymph and tissues were identified as Stenotrophomonas maltophilia and Aeromonas veronii based on biochemical and 16S rDNA sequence analysis. The LD50 values of HOP3 and GL1 were found to be 2.45 × 106 CFU/g (body weight) and 2.24 × 105 CFU/g (body weight) respectively. Histopathology of H. cumingii infected with S. maltophilia and A. veronii displayed degeneration of muscle fibres and gill necrosis. We tested the antibiotic susceptibility of the two isolates and found that HOP3 was multidrug-resistant. Growth optimization study revealed that both isolates remained surviving across wide environmental ranges. Our data lay the foundation for the pathogenic mechanism of mussel bacterial diseases, and they also suggest that effective control measures are worth further investigation.