Tuberculosis remains a global disease, killing over 2 million people each year. India accounts for two-third of the global total i.e. 26%. A good, fast, and economical test to diagnose a disease is urgently needed so that effective treatment can begin as soon as possible. Various investigations can be done for TB diagnosis and these include clinical suspicion, Chest imaging, acid-fast bacilli staining, MTB culture, serological methods and Assays for amplification of nucleic acids. For developing countries like India due to the enormous number of patients and budget restrictions, the assessment of a quick and low-cost diagnostic procedure is critical. A present prospective study was undertaken to compare Ziehl-Neelsen stain with Fluorescent stain microscopy in detecting of Mycobacterium tuberculosis in TB patient’s sputum samples. Among 274 sputum samples collected from suspected TB cases, 50 (18.2%) were positive by ZN and 116 (42.3%) were positive by fluorescent microscopy. The sensitivity, specificity, Positive predictive value (PPV) & Negative predictive value (NPV) of FM microscopy was 98%, 70%, 42%, and 99% respectively. FM microscopy was superior to ZN microscopy in detecting pulmonary tuberculosis cases as it could detect 24.1% more positive cases than ZN staining. Fluorescence staining provides better sensitivity and specificity and can detect accurately more paucibacillary cases hence is of diagnostic value and can help in the early treatment of pulmonary tuberculosis.