Hirudo nipponia is not only an important economic pillar for farmers, but is also a precious raw material for medicinal materials. However, in recent years, H. nipponia suffered from diseases with symptoms including systemic edema and hyperemia. It has not yet been demonstrated which pathogen causes this disease and whether this could be transmitted to humans. In this study, Klebsiella pneumoniae was isolated and identified from diseased H. nipponia and the pathogenicity of the isolated strain was confirmed. Furthermore, by comparing the sequence of the pathogen isolated from leeches to the same pathogen infecting humans, we identified that the isolated strain is a threat to human health. This work emphasizes the importance of the first discovery of pathogenic bacteria from leeches similar to human pathogens, as well as the need for identifying comorbidities for both humans and aquatic animals.