A comparative study on molecular detection of Bursaphelenchus xylophilus was conducted in this paper. Specific amplification PCR, ITS-PCR-RFLP and real time PCR were used in molecular detection of B. xylophilus. According to detection time, detection accuracy and operation skills, this paper summarized following conclusions: (1) Specific amplification PCR is used widely up to now because of its simple operation and low costs; (2) ITS-PCR-RFLP can be used to identify physiological race, being more accurate than Specific amplification PCR, however it takes long time to operate, it can be used for differentiation of population of B. xylophilus and species identification; (3) Real-time PCR takes short time to operate, has a high accurate results, and it’s easy to operate. However it needs specific instruments which are very expensive. It should be better used in quarantine of B. xylophilus.