Abstract: The effects of two oxygenation methods including micro-nano aerated aerator and waterwheel aerator in the process of sturgeon culture were compared and studied in this paper, and the high-throughput sequencing technology was used to analyze the effects of different oxygenation methods on the structure of dominant bacteria and potential pathogenic microorganisms in the aquaculture water, and the correlation between the concentration of dissolved oxygen and the relative abundance of potential pathogenic microorganisms was also analyzed. The results showed that the structure of dominant bacteria in the sturgeon aquaculture water under the micro-nano aerated aerator and the waterwheel aerator was basically the same, and nine kinds of potential pathogenic microorganisms (genus level) were detected in the sturgeon aquaculture water under the two kinds of aeration. Among them, the relative abundance of potential pathogenic microorganisms Acinetobacter, Aeromonas, Clostridium, Flavobacterium, Mycobacterium and Pseudomonas in the micro-nano aerated aerator was lower than that in the aquaculture water with waterwheel aerator. But the difference was not significant (P≥0.05). The results of correlation analysis showed that the potential pathogenic microorganisms Parachlamydia and Rickettsia were significantly positively correlated with the dissolved oxygen concentration in the aquaculture water (P<0.05).