There is growing awareness of the critical role of microbiomes for marine life. However, we lack an understanding of how climate change may affect the microbiome, particularly in valuable aquaculture species. We exposed nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) to predicted warming (ambient = 24°C, elevated = 28 °C) and ocean acidification (ambient pCO2= 400, elevated pCO2 =1000 µatm) for four weeks. The haemolymph bacterial microbiome was characterised using 16S rRNA (V3-V4) gene sequencing and oyster oxygen consumption was measured. Microbiomes were altered by climate change, with this effect dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial β-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Changes in the oyster microbiome were correlated with oyster metabolic rates, suggesting that physiological changes in the oysters triggered by warming and acidification may drive changes in the microbiome. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future adaptive breeding programs to enhance resilience should consider the links between physiology and the microbiome.