The rhizoplane bacterium Lysobacter sp. SB-K88 suppresses damping-off disease in sugar beet and spinach caused by Aphanomyces cochlioides through characteristic plant colonization and antibiosis. Interaction of the pathogen and SB-K88 on potato dextrose agar medium revealed remarkable curly growth, excessive branching, and inhibition of mycelial growth of the pathogen. This study elucidated the mode of antagonism of SB-K88 by detecting changes in ultrastructure and organization of cytoskeletal filamentous actin (F-actin) network in the affected hyphae and zoospores of A. cochlioides. Transmission electron microscopy aided in visualization of significant ultrastructural alterations including invagination of membrane, disintegration or necrosis of cell wall, accumulation of excessive lipid bodies, electron-dense enlarged vacuoles, and degradation of cytoplasm in the SB-K88-induced excessively branched and curled hyphae. Confocal laser scanning microscopy confirmed the role of SB-K88 or its metabolites in severe disruption of the organization of F-actin networks in both hyphae and zoospores of A. cochlioides. An inhibitor of actin polymerization, latrunculin B, also exhibited similar disruption of F-actin organization in the hyphae and zoospores of A. cochlioides. These results suggest that the inhibitory effect of Lysobacter sp. SB-K88 on A. cochlioides is likely due to a combination of F-actin disruption and ultrastructural alterations in the zoospore and hyphal cells.