We observed that 2,4-diacetylphloroglucinol (DAPG), a major antimicrobial metabolite produced by a rhizoplane bacterium Pseudomonas fluorescens ECO-001 inhibited mycelial growth of a damping-off phytopathogen Aphanomyces cochlioides AC-5 through inducing excessive branching and curling in the hyphae. This study aimed to unravel the mode of action of DAPG caused excessive branching, curling and growth inhibition of AC-5 hyphae by detecting localized changes in the cortical filamentous actin (F-actin) organization by rhodamine-conjugated phalloidin. Confocal laser scanning microscopic observations revealed that both living bacteria and DAPG severely disrupted the organization of F-actin in the A. cochlioides hyphae in a similar manner. Furthermore, an inhibitor of F-actin polymerization, latrunculin B also induced similar growth inhibition, excessive branching and caused disruption of F-actin in the AC-5 hyphae. Our results suggested that growth inhibition and excessive branching induced in A. cochlioides by DAPG is likely to be linked to the disruption of F-actin cytoskeleton in the affected hyphae. This is the first report on disruption of cytoskeleton of a eukaryotic A. cochlioides by a well-known biocontrol metabolite DAPG secreted from a prokaryotic bacterium ECO-001.