<b>Background/Objectives</b>: This study evaluated the concordance between sputum and bronchoscopic specimens in diagnosing nontuberculous mycobacteria (NTM) pulmonary disease. <b>Methods</b>: We retrospectively analyzed patients with NTM isolated from respiratory specimens between 2010 and 2022. Our analysis assessed species concordance across the two diagnostic methods and compared clinical outcomes between patients with multiple positive cultures and those with a single positive culture. <b>Results</b>: A total of 400 patients were included, 100 of whom underwent bronchoscopy. Among these, 61 demonstrated concordant NTM species between sputum and bronchoscopic specimens, while 38 had NTM cultured from only one source. One patient showed a discordant result, with <i>Mycobacterium abscessus</i> isolated from bronchoalveolar lavage and <i>Mycobacterium avium</i> from sputum. Multivariate analysis identified several factors associated with radiologic progression or the need for treatment: body mass index (HR, 0.847; 95% CI, 0.794-0.902; <i>p</i> < 0.001), membership in the single-isolation group (HR, 0.400; 95% CI, 0.184-0.871; <i>p</i> = 0.021), and fibrocavitary radiologic type (HR, 2.318; 95% CI, 1.470-3.655; <i>p</i> < 0.001). <b>Conclusions</b>: Only a small number of cases showed different NTM species identified by sputum and bronchoscopy.