[Objective] In order to investigate a forest musk deer's death, we collected the musk deer's lung tissue to isolate and identify bacteria. [Methods] We identified the strains by bacterial isolation and purification, biochemical test and 16S rRNA sequence analysis. Then, we designed the whole genome and cytolethal distendin toxin subunit B analysis to learn the drug resistance and pathogenicity of the isolated strain. [Results] First, a gram-negative strain was isolated from the lungs of the musk deer, and identified as Bordetella trematum and named as ZL0001. It was an intracellular parasitic bacterium containing cytolethal distendin toxin subunit B. According to drug sensitivity test, the isolate was sensitive to ampicillin but resistant to amtriaxone. The average nucleotide identity values of the strain compared to other Bordetella trematum were >97%, and the genome size was 4350644 bp. In the whole-genome, 22 drug-resistant genes were found. Moreover, the genome contains 63 virulence genes that participated in many processes, such as iron intake. [Conclusion] Bordetella trematum was isolated in the respiratory tract of forest musk, and proved as intracellular bacterium.