Abstract: Using HHT method,the paper analyzed the wing vibration sound of two different strain of fruit flies in the same species.It extracted effective characteristics of fruit fly's wing vibration sound,which contained ratios of first ten IMF and signal total energy,the relative energies of low-frequency stage,middle-frequency stage and high-frequency stage in HH spectrum.Then,the paper designed BP neural network to identify different strain of fruit flies.The experiment result indicated that it was feasible and effectivethe method of extracting features by HHT and identifying different strain of fruit flies by neural network .And it provided a new idea and technique for further discrimination of intraspecies relationship of fruit fly.