Abstract: A branch canker disease was observed in Jiagedaqi district, Heilongjiang Province, China, in July 2019. The diseased branches initially appeared light red to reddish brown with light brown to dark brown sunken lesions, produced many gray-black to dark-black bumps in a later stage. In order to determine the pathogen species causing branch canker disease of Quercus mongolica and provide theoretical basis for targeted control, the pathogenic bacteria were isolated and purified by single spore separation method. Morphological characteristics were observed and the conidia size were measured and recorded. The rDNA-ITS, EF1-α, and LSU genes were sequenced and manually edited and aligned using MEGA to construct phylogenetic trees. According to Koch’s rule, the disease was inoculated and the pathogen was isolated again from inoculated shoots. In the inoculation experiment, only the burn group showed typical symptoms, indicating that the pathogen could not penetrate the epidermis or invade through stomata under natural conditions, and it was mainly occurring in young branches and weak branches of Quercus mongolica, which was a weak parasitic disease. Combined with morphological and phylogenetic analysis, the results showed that Cytospora ceratosperma was the pathogenic bacterium of Quercus mongolica and Quercus mongolica was the new host of C. ceratosperma in China.