Pacific oyster mortality syndrome (POMS) in Pacific oysters Crassostrea gigas is defined by mass mortality with Ostreid herpesvirus I (OsHV-1). In this study the association of Vibrio species with oysters before, during and after POMS events was investigated at population level to clarify their involvement with OsHV-1 in mass mortality events in the Georges and Hawkesbury River estuaries, Australia. In the POMS affected Georges River estuary, three patterns were observed concurrently at different sites: i) Vibrio counts and OsHV-1 DNA concentrations increased in adults and spat as mortalities started then decreased as mortalities stopped ii) bacterial counts increased in spat but not in adults associated with mortalities due to OsHV-1 iii) bacterial counts increased in the absence of mass mortality or high concentrations of OsHV-1 DNA. Although almost half of the 120 bacterial isolates were identified as an unknown Vibrio species belonging to the Splendidus clade with two predominant biotypes (A and H), there was no association between biotype and mortality. Concurrently in the Hawkesbury River estuary, neither mortality nor OsHV-1 were found, Vibrio counts fluctuated significantly and of 84 isolates identified, V. alginolyticus, V. parahaemolyticus and unidentified Vibrio sp. dominated; only five Splendidus clade isolates were identified. However, when POMS emerged in the Hawkesbury River estuary, the Splendidus-clade isolate became the dominant bacterial species. Mortality also occurred there without OsHV-1 and the dominant bacteria then were V. alginolyticus and V. harveyi, but the Splendidus-clade isolate was not detected. None of the bacterial species were specifically associated with POMS, although the Splendidus clade isolate increased in prevalence after POMS emerged in the Hawkesbury River estuary. V. aestuarianus was not detected in this study. While the findings suggest that bacterial proliferation follows infection with OsHV-1 in POMS, this was not a consistent feature. The number and diversity of bacteria within oyster tissues varied over time, between estuaries, between sites within an estuary and were associated with flooding, growing height, the age of oysters, mortality and OsHV-1.