Background: Nontuberculous mycobacteria (NTM) treatment constitutes a macrolide-based antibiotic regimen in combination with aminoglycosides for Rapid-Growing mycobacteria (RGM), and rifampicin for Slow-Growing mycobacteria (SGM). Mutations in the anti-NTM drug target regions promote NTM evolution to mutant strains that are insusceptible to NTM drugs leading to treatment failure. We, therefore, described the mutation patterns of anti-NTM drug target genes including rrl, rrs, and rpoB in NTM isolates from Kenya. Methods: We carried out a cross-sectional study that included 122 NTM obtained from the sputum of symptomatic tuberculosis-negative patients in Kenya. All the 122 NTM underwent targeted sequencing of the rrl gene. The 54 RGM were also sequenced for rrs, and the 68 SGM were sequenced for rpoB genes using ABI 3730XL analyzer. The obtained sequences were aligned to their wild-type reference sequences for each gene using Geneious then mutations were identified. Pearson chi-square at 95% confidence interval tested the association of NTM to mutation patterns for each gene. Results: Twenty-eight (23%) of the NTM were resistant to at least one of the antibiotics used in the macrolide-based treatment. Twelve (10.4%) of NTM were macrolide resistant, with 7(58.3%) of RGM and 5(41.7%) of SGM having mutations in the rrl gene. For ten (83.3%) NTM, mutations were found at position 2058, while for two (16.6%) NTM, mutations were found at position 2059. Six (11.1%) of the 54 RGM exhibited mutations in the aminoglycoside target gene rrs at location 1408. Ten (14.7%) of the 68 SGM were resistant to rifampicin, with 40 percent having mutations at codon 531 in the rpoB gene. Conclusion: We demonstrated a significant level of drug resistance for macrolides, aminoglycosides and rifampicin in NTM isolated from symptomatic TB negative patients in Kenya.