Abstract: Rapid and reliable detection of pathogens is critical for the prevention and treatment of animal epidemic diseases. In recent years, with the development of automation, high throughput and current use of molecular detection, various new molecular diagnostic techniques based on PCR amplification are proved to be more fast, specific, sensitive, and reliable in pathogen detection compared to the traditional detection methods. As the new types of molecular diagnostic techniques gradually mature, they are promising for broad application in different field, such as animal disease detection and identification, and entry-exit inspection and quarantine and so on. Furthermore, a wide range of epidemiology can be conducted with the new molecular diagnostic techniques, which is helpful for taking measures for scientific prevention and control of animal epidemics.