Many problems caused by blooms of cyanobacteria have been reported, and the frequency of the blooms seems to be increasing. Algae-lysing bacteria have the ability to kill water bloom organisms. In the course of studies on the interactions between blue-green algae and algae-lysing bacteria, a strain of Sphingomonas sp. was found to produce a novel pentapeptide, argimicin A (1), with high algaecidal activity against Microcystis spp. This communication describes the isolation and structural elucidation of argimicin A. The producer was isolated from Lake Biwa and classified into Sphingomonas sp. via taxonomic studies and 16S rDNA analysis. The compound was isolated through Diaion HP-20 column, Toyopearl HW-40 column, and HPLC purification. From FAB-MS, HRFAB-MS, and 13C-NMR data, the molecular formula of 1 was determined to be C32H62N12O8. Structural elucidation via NMR (1H COSY, TOCSY, HMQC, HMBC) revealed that 1 is a pentapeptide consisting of N-trimethyl-Arg as the N-terminal residue, two Val, 4-hydroxy-NG-methyl-Arg, and N-methyl-Gln as the C-terminal residue. Argimicin A exhibits strong activity against Microcystis viridis NIES-102 (12 ng/ml) and M. aeruginosa NIES-298 (100 ng/ml), while showing no effects on Escherichia coli, Bacillus subtilis, and Chlorella vulgaris. It is also active at 100 ng/ml against environmental non-axenic cyanobacteria. Compared to known algaecides (e.g., L-lysine with a minimum inhibitory concentration of 5 μg/ml against Microcystis spp.), argimicin A has higher potency and might be effective in natural aquatic environments. Further studies on the stereochemistry and ecological role of 1 in aquatic ecosystems are under way.