The spectra of root, stem, leaf of two hydrophytes (Oenanthe javanica and Iris pseudacorus) with CK, low, medium and high metal treatment (Cr, Fe, Mn and Zn) were determined directly, fast and accurately by Fourier transform infrared (FTIR) spectrometry with OMNI-sampler. The results showed that the peak shape of plant component remained invariable basically when absorbing heavy metals. Significant absorption peak shifts of some functional groups such as hydroxy groups (3 328-3 361 cm-1), carboxyl groups (1 402-1 440 cm-1), and acidamide groups (1 620-1 645 cm-1)can be seen when they participated in the process of absorbing heavy metals. The varieties of organic characteristic peaks were also capable of reflecting physiology and metabolism changes. With increasing heavy metal concentration, the absorption intensity of most root characteristic peaks correlated with physiology decreased significantly for the two hydrophytes, but it was decreased for stem, leaf characteristic peaks of Oenanthe javanica. The absorbance of stem, leaf was bigger than the control for different heavy metals for Iris pseudacorus. To sum up, although two hydrophytes could endure certain concentration of heavy metals, the tolerance of Iris pseudacorus was greater than that of Oenanthe javanica. With strong identifying ability, exact determination results and fast response function, the application of FTIR method has been popularized gradually in the field of environmental science. Recently, greater progress has been made in the study and use of FTIR in the fields of environmental accident emergent monitoring, environmental monitoring and environmental chemistry research. The infrared spectra could also be widely used to monitor changes in chemical composition of plant parts under stresses and environmental restoration and supply the best evidence for phytoremediation. This method was an important tool for detecting unknown pollutants and environmental monitoring.