The invention discloses a novel beta-1,6-glucanase, an encoding gene thereof, and applications of the encoding gene. The invention provides the beta-1,6-glucanase gene belonging to the glucoside hydrolase system, wherein the nucleotide sequence of the beta-1,6-glucanase gene is shown in SEQ ID NO.1, and the protein (amino acid) sequence of the encoded outer membrane glucoside hydrolase is shown in SEQ ID NO.2. The beta-1,6-glucanase can effectively prevent the infection of plant pathogenic fungi to plants. An engineered strain established by the gene realizes the prokaryotic expression of the beta-1,6-glucanase gene, and verifies the function of the glucoside hydrolase of the beta-1,6-glucanase gene, the result shows that GluM can effectively inhibit the germination of rice blast spores, and decompose the rice blast spores. After the beta-1,6-glucanase gene is transplanted into the dicotyledonous model plant arabidopsis thaliana and the monocotyledonous model plant rice, the result shows that the obtained transgenic plants have good anti-infection effects for grey mould and rice blast.