The rpoB gene based sequencing analysis enabled not only the detection of rifampin resistant Mycobacterium tuberculosis, but also the differentiation of species in the genus Mycobacterium. In the present study, we applied the method to 68 isolates of M. tuberculosis (29 from initial treatment cases and 39 from recurrent cases) and 11 clinical isolates of nontuberculous mycobacteia (NTM) isolated from patients in Jeju island. Among rifampin resistant M. tuberculosis, two of 29 strains isolated from patients of initial cases (6.9%) and five of 39 strains isolated from patients of recurrent cases (12.8%) were confirmed to have rifampin resistant genotypes harboring mutations in $rif^r$ region of the rpoB gene. In NTM strains, M. fortuitum complex was the most frequently isolated species at the frequency of 54.5% (6/11).