Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis which has a high impact in endemic countries, with an estimated average 1.5 million death per year. TB is a curable disease, three lines of treatment are available, but the emergence of drug resistance represents a major challenge to management and control. The present study investigates mutations in putative isoniazid (INH) resistance genes, katG, InhA and InhA promotor and ahpC, in a population sample of isoniazid-sensitive (INHS ) and resistant (INHR) Mycobacterium tuberculosis in Oman. A Hundred M. tuberculosis isolates, INHS (n=57) and INHR (n=43) were collected from nationals (n=32) and expatriates' patients (n=68) from foreign countries. Mutations were identified by amplifying and DNA sequencing of the whole size of each gene. The most polymorphic gene was KatG (11 alleles), followed by InhA and its promoter (6 alleles) and ahpC (3 alleles). Mutations affecting katG, the InhA promoter and open reading frame and ahpC were found in, 71.4%, 30.2% and 4.65% of INHR isolates, respectively, and in 61%, 0%, and 3.5% of INHS strains, respectively. The frequency of mutations in KatG (P<0.01) and InhA (P<0.01) were significantly linked to the INH resistance profile, however, ahpC mutations were not. The common KatG mutation 315T was associated with INHR , while multiple mutations in the examined genes were associated with increased probability of INH resistance. Multi-locus haplotypes carrying KatG 463L plus KatG 315T existed at a significantly higher prevalence among INHR isolates than haplotypes-carrying KatG 315T alone, suggests a cumulative effect of mutations and a role of epistasis in stabilizing INH resistance. Mutations of the above genes were distributed evenly among M. tuberculosis isolates causing pulmonary and extra-pulmonary. There was no difference in the proportion of mutations among M. tuberculosis causing pulmonary TB (54/83, 65%) compared to those causing extra-pulmonary TB (11/17, 64%). Multi-locus haplotypes of KatG, InhA and ahpC were shared between Omanis and expatriates, with no significant differences. Genetic differentiation analysis, including spoligo loci, demonstrated close genetic background of M. tuberculosis isolates infecting Omanis and expatriates; this suggests a possible circulation of drug resistance strains between the two groups. The M. tuberculosis isolates examined in the presents study belong to 9 Spoligo-families with variable response to INH. The frequent spoligotypes were CAS (26 %), EAI (25%), Beijing (17%), and T (15%). The CAS and T families were more common among INHS M. tuberculosis isolates, seen at a prevalence of 17% and 8% respectively, while, EAI family (13%) was more frequent among INHR isolates. However, there was no association between INH response and spoligotype characteristic among the examined isolates. In addition, mutations of the three genes were prevalent among Beijing, EAI and CAS spoligo families. In summary, the present study demonstrated high rates of KatG (katG 315T ) and InhA (- 15T and -17T InhA promoter ) mutations in INH resistant M. tuberculosis isolates in Oman, 70% of unrelated isoniazid-resistant isolates could be identified by analysis of just two loci (katG 315T and -15T and -17T InhA promoter). The shared INHR M. tuberculosis haplotypes, with related genetic background among Omanis and expatriates warrant further investigation to asses if there was a transmission of resistant strains between the two groups.