Huperzia serrata is an important medicinal plant. This species is rich in inner-specific variation with various closely related species, and their individuals are also small with few identification characters. In the present paper, the method of Fourier transform infrared spectrometer with an OMNI collector was applied to obtaining the infrared spectra of 16 leaf samples including Huperzia serrata and its five closely related species (Huperzia sutchueniana, Phlegmariurus mingchegensis, Lycopodium japonicum, Selaginella doederleinii, Selaginella heterostachys). Based on the indices of wave number-absorbance, the differences of the 16 infrared spectra were compared by the method of Principal Component Analysis (PCA). The results showed that there is good correspondence between the position relationship of PCA three-dimensional plot of the samples based on the indices of wave number-absorbance of FTIR spectra and their phenetic relationship. Therefore, the infrared spectra could be applied to identifying the samples of Huperzia serrata and its closely related species.