In 1998, a 51-year-old woman was diagnosed with Mycobacterium avium infection on the basis of chest radiographic findings, positive smear test results, and positive results of polymerase chain reaction (PCR) specific for Mycobacterium avium DNA in bronchial lavage fluid. Antimycobacterial therapy was administered for 11 months, and the chest radiographic findings improved. In 2001, re-treatment was performed because radiographic findings indicated exacerbation of disease and poor response. After 2005, the patient remained both smear and culture positive for mycobacterium. However, the precise species could not be identified using PCR and DNA-DNA hybridization, and her left lung lesions gradually worsened. The culture isolate was subjected to DNA analysis with PCR amplification and sequence analysis; this ultimately revealed the presence of Mycobacterium lentiflavum. Combination antimicrobial therapy was administered for 10 months. The patient's symptoms were alleviated, and the radiographic appearance remained stable.