The gene for histone-like protein (hupB [Rv2986c]) of Mycobacterium tuberculosis has been identified as a singular target which allows differentiation of two closely related mycobacterial species, namely, M. tuberculosis and M. bovis of the MTB complex, by a PCR assay. The N and S primer-generated PCR amplicons differed in M. tuberculosis and M. bovis; these amplicons were determined to be 645 and 618 bp, respectively. This difference was localized to the C-terminal part of the gene by using primers M and S. The C-terminal PCR amplicons of M. tuberculosis and M. bovis were determined to be 318 and 291 bp, respectively. The differences in the C-terminal portion of the gene were confirmed by restriction fragment length polymorphism analysis and sequencing. Sequence analysis indicated that in M. bovis there was a deletion of 27 bp (9 amino acids) in frame after codon 128 in the C-terminal part of the hupB gene. In the present study 104 mycobacterial strains and 11 nonmycobacterial species were analyzed for hupB gene sequences. Of the 104 mycobacterial strains included, 62 belonged to the MTB complex and 42 were non-MTB complex strains and species. Neither the hupB gene-specific primers (N and S) nor the C-terminal primers (M and S) amplify DNA from any other mycobacteria, making the assay suitable for distinguishing members of the MTB complex from other mycobacterial species, as well as for differentiating between members of the MTB complex, namely, M. tuberculosis and M. bovis.Early and reliable detection of pathogenic mycobacteria in clinical samples is a major limitation in the control of human tuberculosis. At present, a battery of tedious tests (microbiological, biochemical, etc.) requiring more than several days or weeks are routinely used to identify clinical mycobacterial isolates. The criteria used for the differentiation of Mycobacterium tuberculosis and M. bovis have been colony morphology, nitrate reduction, niacin test, and sensitivity or resistance to pyrazinamide. Deviations from standard patterns in all of the above tests have been reported, making it virtually impossible to differentiate between M. bovis, M. tuberculosis, and M. africanum (12, 34, 38, 48). The high degree of variability in the phenotypic characteristics has made it important to develop reliable techniques to distinguish between members of the Mycobacterium tuberculosis and M. bovis (MTB) complex (22,41). Techniques based on the amplification of mycobacterial DNA sequences by PCR have been introduced in many laboratories as a promising alternative rapid, sensitive, and specific detection of M. tuberculosis in clinical specimens (2,7,14).Novel targets have been exploited for diagnostic purposes by using PCR, namely, the devR response regulator gene (42, 43), rRNA (5), selected chromosomal fragments (3,18,25,29), genes coding for the 65-kDa heat shock protein (36), the 38-kDa protein antigen (44), the dnaJ gene (47), and insertion sequences such as IS6110, IS990, and IS1081 (1,15,16,23); these are all examples of diverse targets that ...