In this paper, the Fourier transform infrared spectroscopy (FTIR) of the seeds of 80 herbaceous species, including subspecies and varieties of 8 families, were obtained using the method of FTIR with an OMNI collector. The peak values of FTIR between 3 100 cm-1 and 900 cm-1 were recorded and analyzed by the method of cluster analysis. The results were as follows: (1) Seeds of 80 species or subspecies could be classified into two groups. Group I included the seeds of Gramineae, Cyperaceae, Polygonaceae and Amaranthaceae, and Group II included the seeds of Compositae, Euphorbiaceae, Brassicaceae and Umbelliferae.(2) Only FTIRs of the seeds of Brassicaceae were clustered together in the dendrogram, while those of the other families all appeared farraginous.(3) Among FTIRs of the 11 groups of the congeneric species, 8 groups were clustered with other genus species, and 6 out of 7 groups of conspecific seeds appeared farraginous in the dendrogram. Therefore, the values of the application of FTIR to study the plant taxonomical relationships and to identify plant species are limited. It is suggested that the spectra of other taxa with distant taxonomical relationship should be included to evaluate the reliability of the method. Also, experimental replications should be highlighted, the significant differences between different materials should be confirmed by statistical tests in the application of FTIR to discriminate species or samples.