Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic infections. In this study, lung pathogenic K. pneumoniae (LPKP) was isolated and identified from suppurative pneumoniae in forest musk deer by conventional methods and by 16S ribosomal RNA sequence analysis. Median lethal dose and histopathologic analysis were used to demonstrate pathogenicity of the organism in mice. Furthermore, a draft genome of LPKP was sequenced, and its virulence genes were detected. One hundred and twenty-two virulence genes encoded determinant of capsule polysaccharide (CPS), lipopolysaccharide, fimbriae, outer membrane proteins, iron acquisition, and urease. In particular, 20 CPS-related genes were highly conserved in LPKP, K. pneumoniae U, K. pneumoniae NTUH-KP35, and K. pneumoniae KP-1. All of the strains were identified as capsular type K54. This is the first report of capsular type K54 K. pneumoniae causing suppurative pneumonia in an animal. The results of this study provided the basis for understanding the pathogenicity of LPKP and laid a foundation for the development of vaccines for the capsular type K54 K. pneumoniae disease.