We evaluated the association between 16S rRNA gene (rrs) mutations and susceptibility in amikacin-resistant nontuberculous mycobacterial (NTM) clinical isolates in NTM- pulmonary disease (PD) patients. Susceptibility was retested for 134 amikacin-resistant isolates (minimum inhibitory concentration [MIC] ≥64 µg/ml) from 86 patients. Amikacin resistance was reconfirmed in 102 NTM isolates from 62 patients with either Mycobacterium avium complex-PD (MAC-PD) (n=54) or M. abscessus-PD (n=8). MIC and rrs mutations were evaluated for 318 single colonies from these isolates. For the 54 MAC-PD patients, rrs mutations were present in all isolates (obtained from 31 patients) with an amikacin MIC ≥128 µg/ml, but only in a few isolates (from three of 23 patients) with an MIC=64 µg/ml. For the eight M. abscessus-PD patients, all amikacin-resistant isolates (MIC ≥64 µg/ml) had rrs mutations. Of amikacin resistance isolates, A1408G mutation (n=29) was most common. Two novel mutations, C1496T and T1498A, were also identified. The culture conversion rate did not differ by amikacin MIC (20% for MIC=64µg/ml vs. 7% for MIC ≥128 µg/ml, p=0.468). In conclusion, all amikacin-resistant M. abscessus isolates had rrs mutations, but in MAC isolates showing relatively low resistance (MIC=64µg/ml), rrs mutations were infrequently identified.