It has been reported that aquatic vascular plants such as Myriophyllum spicatum and Ceratophyllum demersum have allelopathic effects green algae and bacteria. In this study, I intended to figure out allelopathic activities of various aquatic plant species and to compare their inhibition effects against bacteria based on different methods. Total of 34 dried samples from 26 plant species were extracted by 80 % methanol. The antioxidant test was carried out with radical scavenging activity method using DPPH as a control. Bioassay experiments were carried out against Escherichia coli and Microcystis aeruginosa., Fourier Transform Infrared (FT-IR) spectra were profiled over the 4,000∼650 cm-1 and processed using the spectrum GX in ATR mode. The cell density was measured of optical density on 550 nm every hour to get E. coli growth pattern then E. coli was cultured at the conditions of LB medium/ 37 ℃/ 150 rpm. M. aeruginosa was cultured at the conditions of L16 medium/ 25 ℃/ 150 rpm/ 2000 lux at the growth chamber of, Light/Dark cycle (16/8). Absorbance (O.D. 610∼800 nm) was measured on 2 days and calculated by the concentration of chlorophyll-a. Among the aquatic plants, Brasenia schreberi, Persicaria amphibia and Trapa japonica showed higher DPPH radical scavenging activities than other palnts. B. schreberi, P. amphibia, T. japonica and Myriophyllum spicatum growth showed more strong inhibition activities against cyanobacteria than other plants. Among two activities were analyzed to show a positive correlationship. However, most of methanol extract from aquatic plants showed low growth inhibition activity against E. coli except B. schreberi extract. FT-IR analyses showed that this method could be useful for fast screening techniques instead of bioassay because verified positive correlation was found between growth inhibition activity against M. aeruginosa and FT-IR spectra of methanol extract of aquatic plants. B. schreberi extract showed the highest growth inhibition activity among 26 aquatic plants based on bioassay results so that I tried to test the growth inhibition activities of methanol extracts from different part of plants against M. aeruginosa. As a result, leaf and gelly extracts of B. schreberi showed higher inhibition activities than other parts. This study suggest that some of aquatic plants has allelopathic activities against cyanobacteria and using FT-IR profiles would be helpful for a fast screening of their activities.