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Enzymes that degrade fungal cell walls and the resulting oligosaccharides are promising weapons to combat plant fungal disease. In this study, we identified a novel endo-chitosanase, Aq CoA, from Aquabacterium sp. A7-Y. The enzyme showed a specific activity of 18 U/mg toward 95% deacetylated chitosan at pH 5.0 and 40 °C. Aq CoA also showed activity toward sodium carboxymethylcellulose, indicating substrate promiscuity. Aq CoA hydrolyzed chitosan into chitooligosaccharides (CoA-COSs) with degrees of polymerization (DPs) of 3-5 but showed no activity toward CoA-COSs with DPs <6, indicating an endo-type activity. At 2.5 μg/mL, Aq CoA inhibited appressorium formation of Magnaporthe oryzae ; the produced CoA-COSs also inhibited the growth of M. oryzae and Fusarium oxysporum . Furthermore, CoA-COSs acted as immune elicitors in rice by inducing the reactive oxygen species burst and the expression of defense genes. These results demonstrated that Aq CoA and its resulting CoA-COSs might be effective tools for protecting plants against pathogenic fungi.