TB is a major global health problem and an important cause of morbidity and mortality in the world. TB is the ninth leading cause of death in the world despite the presence of several treatment strategies to manage the disease. This study was prepared to determine the genotyping of M. tuberculosis isolate of pulmonary and extra pulmonary tuberculosis. Samples were collected from (612) tuberculosis patients,(409) of them were pulmonary tuberculosis and (203) of them were extrapolmonary tuberculosis subjects atthe Specialized Chest and Respiratory Disease Center/National Reference Laboratory for Tuberculosis (NRL) in Baghdad, during the period from 1st of May 2019 to 1st of October 2019. SNP genotyping of 75 M. tuberculosis DNA samples (50 PTB and 25 EPTB) exhibited that 98 isolates were present, indicating that some of patients had two isolates or more (mixed of infection) and the major phylogenetic lineages of M. tuberculosis in city of Baghdad were: 18 (18.4%) of Lineage 1, 2 of Lineage 2, which was the lowest frequent, 40 (40.8%) of Lineage 3, which was the mostincidence, 26 (26.5%) of Lineage 4, the residual samples 12 (12.2%) could not be assigned to any recognized Lineages thus considered as unknown genotypes. Our study confirmed that East-African-Indian (Lineage 3) lineage was most prevalent in Baghdad for pulmonary and extrapulmonary tuberculosis in Iraqi patient.