We conducted a 7-d co-existence experiment to verify the inhibitory activity of an aquatic vascular plant, Myriophyllum spicatum, on the cyanobacterium Microcystis aeruginosa, and to screen for allelopathic compounds. Plants were placed on a modified solid M4 medium while M. aeruginosa was cultured in an L16 liquid medium. Our treatments included rearing Myriophyllum spicatum alone (Plant-Only; PO) or with Microcystis aeruginosa (Plant-Cyanobacteria; PCB), as well as an untreated control, or plates with the cyanobacterium alone. In the PCB treatment, M. aeruginosa became transparent in three replicates on the 6th day and in four replicates on Day 7. To make the distinction in Myriophyllum spicatum metabolites between the PO and PCB treatments, we obtained 13 m/z profiles using a 15 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Principle component analyses were performed on those profiles, from which we obtained accurate mass values for selected peaks that had most negative loadings on the first principal component and most positive loadings on the second principal component: 282.06983 and 283.06836. We identified those peaks as $C_7H_{17}N_5O_3S_2$ and $C_{10}H_{12}N_4O_6$, respectively. The Dictionary of Natural Products database suggests that the latter is either oxanosine or xanthosine.