The infectious pathogens against honeybee (Apis mellifera) comprise a heterogeneous group of bacterial, viral, and fungal organisms including Paenibacillus larvae, Deformed Wing Virus (DWV) and Nosema apis. Many species like Paenibacillus larvae, Deformed Wing Virus (DWV) and Nosema apis have been isolated from a number of different continents, e.g. America, Asia and Europe, indicating its wide spread in whole nature. Little is known about the occurrence and distribution in the environment of these pathogens. For a more rapid, systematic and efficient monitoring of each pathogenic species against honeybee in the environment, PCR-based detection systems were developed that allows species-specific identifications of various pathogenic species with one reaction. These could be achieved by selecting specific primers from conserved regions of each species with speciesspecific DNA sequence variations. For the detection of any already known pathogen, well-developed PCR-detection system allows the specific detection of expected pathogenic species based on its specific nucleic acid sequence. Since each pathogenic species delivers a specific PCR-product of different size, bands can be distinguished very easily by simple gel electrophoresis. After the development of real-time PCR system, PCR-based specific detections of honeybee pathogens were dramatically improved their applications, from just detection to quantification of pathogens. These systems, quantitative PCR (qPCR) for the detection of honeybee pathogens, could be distinguished from previous PCR detection on the points of “real-time”, “easy” and “quantitative”. Moreover, very rapid PCR, so-called “Ultra-Rapid Real-Time PCR” were developed recently in field of pathogen-detection. Typical Honeybee pathogens such as Paenibacillus larvae, Israelli acute paralysis virus (IAPV) were successfully detected inner 7 minutes using 30 cycled Ultrarapid PCR. According to development of more rapid apparatus, even 30 cycled, 1 minute PCR seems to be possible. Ultla-Rapid PCR was currently attempted to apply for the direct detection system of all viral pathogens against honeybee from bee-samples and different environmental probes.