Abstract: Sturgeon is rare ancient and diadromous fish. The microbial status of aquaculture environment is closely related to the health of fishes, which has drawn extensive attention. Here, high-throughput sequencing technology was used to determine the community composition and complexity of the microbiota in A. sinensis, A. schrenckii, H. dauricus, and hybrid sturgeon (A. schrenckii ♂×H. dauricus ♀) breeding environment farmed in Chinese sturgeon conservation center. The potential pathogens of their microbial communities were assessed by Real-time fluorescence quantitative PCR technology (RT-PCR). The results demonstrated that the microbiota in cage culture water were dominated by bacteria in the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Planctomycetes, which accounted for 88.81%—93.94% of the sequenced reads in all samples. At the genus level, unclassified genera represented a considerable proportion in all of the experimental samples. Statistical analyses revealed that the diversity of microbial community among the groups did not reach the significant level, and the similarity of the microbial communities was high. The potential pathogenic genera in the culture water were Aeromonas, Acinetobacter, Chryseobacterium, Edwardsiella, Flavobacterium, Pseudomonas and Vibrio. The RT-PCR analyses indicated that A. hydrophila (7406±1892) copies/mL was the most abundant pathogen in sturgeon cage culture water, followed by F. columnar (4889±1649) copies/mL and P. fluorescens (3259±1117) copies/mL. Our results will be the basis for guiding healthy aquaculture of sturgeon and the early warning of pathogenic diseases in the breeding processes.