To investigate the cause of low survival rates of Macrobrachium rosenbergii zoea in a breeding farm, traditional bacterial isolation, culture, and infection experiments were carried out. Survival rates were determined after antibacterial (oxytetracycline) bathing and disinfectant (formalin and allicin) treatments. The microbiota alterations of M. rosenbergii zoea after antibacterial bathing (zoea antibiotic treatment group and berried female antibiotic treatment group) and disinfectant treatments were identified. The results showed the presence of 42 strains of dominant bacteria that were isolated from the zoea; four strains belonging to the genus Vibrio were randomly selected and shown to have different degrees of pathogenicity, indicating mixed infection of Vibrio pathogens in the M. rosenbergii zoea. The use of an antibacterial drug and disinfectant significantly increased survival rates, indicating that bacterial infection was the main cause of the low survival rates of the M. rosenbergii zoea in this farm. High throughput sequencing results showed a decrease of bacterial diversity of the M. rosenbergii zoea after disinfectant treatment (p ≤ 0.05). The relative abundances of the dominant genera (>5%) were as follows: Vibrio was most abundant in the control group (33.52%), whereas values were low in the drug treatment group (zoea 4.9%, berried female 4.6%) and disinfectant group (
