Tuberculosis remains a global threat to public health. Considerable efforts have been made to combat this disease. However, the emergence of Mycobacterium tuberculosis (Mtb) strains resistant to the major anti-tuberculosis drugs especially multidrug resistant (MDR) strains poses a deadly threat to control programs. The present study aims to identify the most common mutations within multidrug-resistant M. tuberculosis Moroccan isolates in order to use them as molecular markers for early and rapid detection of multidrug resistant strains. For that, all M. tuberculosis isolates received during 2002-2003 in the National Reference Laboratory of Tuberculosis in Morocco were subject to drug susceptibility tests for rifampicin and isoniazid and to a PCR probe method to detect specific mutation. Sequencing was performed for all genotypic rifampicin resistant isolates and also for four genotypic isoniazid resistant isolates randomly selected. Out of 187 M. tuberculosis positive cultures, 46 (24.6%) were phenotypically resistant to both rifampicin and isoniazid. Nucleotide mutations in rpoB531, rpoB526, rpoB516, katG315 and inh-15 codons associated with resistance to rifampin (RIF) and isoniazid (INH) were found respectively in 37/46 (80.4%) and 43/46 (93.5%) isolates. Genotypic multi drug resistance was then confirmed in 74% (34/46) isolates. The mutations at codon 315 of katG gene and at codons 531, 526 and 516 of rpoB gene are frequently found in MDR isolates which confirm their strong implication in the development of multidrug resistant tuberculosis. We concluded that these mutations are useful as molecular markers for detection of multidrug resistant isolates but are not yet sufficient to fully predict M. tuberculosis multidrug resistance.