Objective Zebrafish is one of the most widely used model animals for scientific research in the world. The health and quality of zebrafish are the basis for accurate data and reliable results. With the rapid development of zebrafish related research in China, the number of fish diseases in research facilities has been increasing in recent years. However, the research and analysis on these diseases have been lacking. A novel lethal disease, “hole in the head” disease has spread in several zebrafish facilities since 2018, whose pathogen was unrecognized and hard to be controlled. Pathogen identification is urgently needed, and the analysis and advice of health administration are required for the fast-growing field.Methods We necropsied the brain tissue from the “hole in the head” disease zebrafish. After the brain tissue was homogenized, the pathogen was isolated and cultured on brain heart infusion agar (BHIA) plates. The isolated pathogen was analyzed for biochemical characteristics and 16S rDNA homology. The Koch’s Postulate was fulfilled to confirm the pathogen. In addition, we analyzed the zebrafish disease data collected by China Zebrafish Resource Center (CZRC) from 2017 to 2021 and summarized the characteristics of various common diseases.Results The isolated and identified pathogen of the “hole in the head” disease has the same physicochemical properties with Edwardsiella ictaluri, which also fulfilled the Koch’s Postulate. The 16s DNA sequence of this pathogen was highly homologous to Edwardsiella ictalurid. From 2017 to 2021 CZRC has collected 121 disease and fish death cases in Chinese zebrafish facilities. We found that 50.4% fish health problems were directly or indirectly caused by equipment failure and abiotic factors, including 12.39% fish death caused only by improper equipment maintenance and water quality problems. The most lethal problem was gas poisoning. Among all the known pathogens, bacterial pathogens were the most common, accounting for 83.46%, fungal pathogens accounted for 2.47%, and parasitic pathogens accounted for 1.65%. Among all the known bacterial diseases, the opportunistic pathogens of the genus Aeromonas were the most common, followed by Edwardsiella, accounting for 34.65% and 23.76% respectively.Conclusion Edwardsiella ictaluri was isolated and identified as the pathogen of “hole in the head” disease. The highest incidence of zebrafish disease is bacterial infection, and nearly half of zebrafish health problems are caused by abiotic factors. Well-maintained equipment and proper water quality are the most important prerequisites to ensure the health of zebrafish, managements of daily hygiene are the main means to prevent fish diseases, and the prevention of bacterial diseases is the top priority of zebrafish farming.