A Gram-negative bacterium was isolated from the blood of a patient with diabetes mellitus. However, it could not be identified by conventional microbiological methods, and so was characterized by phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Neisseria. Based on the phenotypic and genotypic characteristics, we propose that strain SMC-A9199^T (=KCTC 22696^T=JCM 16127^T) should be classified as a novel species, ‘Neisseria skkuensis’ sp. nov. The patient was further treated with amoxicillin–clavulanate and ciprofloxacin for 3 weeks.