The present study, unique in Tunisia, focused on commensal Neisseriain order to report the cases of infections observed among clinical strains isolated at the National Center of Bone Marrow Transplantation of Tunis, to compare the classical biochemical and genotypic identification techniques of Neisseria spp. and to study their genetic diversity. Only one strain, identified as Neisseria mucosa, was responsible for bacteremia-like infection. Difficulty in the identification of commensal Neisseria at the species level was highlighted with a discrepancy between phenotypic and molecular methods and lack of precise identification by the latter for a large number of strains. Significant genetic diversity was found in commensal Neisseria with high intra-specific variability of the 16S rRNA gene, high heterogeneity of the penA gene and high diversity within the household genes.