Due to immune deficiency diseases (cancer, transplant recipients and HIV) environmental mycobacteria infections are increasing. Forasmuch as the clinical symptons of environmental mycobacteria lung infections and tuberculosis are similar, due to difference of diet therapy between environmental mycobacterium infections and Mycobacterium tuberculosis, it is necessary to identify and differentiate Mycobacterium species. Molecular methods seem to be a useful tool for detection and differentiation of Mycobacterium species