beta-1,6-Glucan plays a crucial role in fungal cell walls by linking the outer layer of mannoproteins and the inner layer of beta-1,3-glucan, contributing significantly to the maintenance of cell wall rigidity. Therefore, the hydrolysis of beta-1,6-glucan by beta-1,6-glucanase directly leads to the disintegration of the fungal cell wall. Here, a novel beta-1,6-glucanase FlGlu30 was identified from the endophytic Flavobacterium sp. NAU1659 and heterologously expressed in Escherichia coli BL21 (DE3). The optimal reaction conditions of purified FlGlu30 were 50degree celsius and pH 6.0, resulting in a specific activity of 173.1 U/mg using pustulan as the substrate. The hydrolyzed products of FlGlu30 to pustulan were mainly gentianose within 1 h of reaction. With the extension of reaction time, gentianose was gradually hydrolyzed to glucose, indicating that FlGlu30 is an endo-beta-1,6-glucanase. The germination of Magnaporthe oryzae Guy11 spores could not be inhibited by FlGlu30, but the appressorium formation of spores was completely inhibited under the concentration of 250.0 U/mL FlGlu30. The disruptions of cell wall and accumulation of intracellular reactive oxide species (ROS) were observed in FlGlu30-treated M. oryzae Guy11 cells, suggesting the significant importance of beta-1,6-glucan as a potential antifungal target and the potential application of FlGlu30. Key points center dot beta-1,6-Glucan is a key component maintaining the rigid structure of fungal cell wall. center dot beta-1,6-Glucanase is an antifungal protein with significant potential applications. center dot FlGlu30 is the first reported beta-1, 6-glucanase derived from Flavobacterium.