The coral reef ecosystem with extremely high value of ecology and economy are the most prominent and representative ecosystem in the tropical ocean. However, coral reef degradation caused by coral diseases has become one of the major threats of coral reef ecosystems. Many microbial pathogens (including bacteria, fungi, and virus) are thought to be closely related to coral disease. Identification of coral pathogens and establishing their rapid detection methods are crucial for epidemiological investigation and formulating of prevention and control measures of coral diseases. This paper mainly reviews the related microbial pathogens of coral diseases and research progress in molecular diagnosis techniques for coral pathogens.