Tobacco-related diseases are the foremost cause of death globally. This research investigates the impact of smoking on lung function and the colonization of respiratory pathogens in asymptomatic smokers. Forty male smokers and forty age-matched non-smoker controls aged between 25-45 years were recruited. Nicotine dependence was evaluated using the Fagerstrom test for nicotine dependence questionnaire, while cumulative tobacco consumption was measured in pack-years. Pulmonary function test (PFT) was performed and morning sputum samples were collected for the molecular detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis using the conventional polymerase chain reaction (PCR) method. PFT parameters  FVC (L), FEV₁ (L), FEV₁/FVC%, PEFR (L/m) and FER_25-75% (L/s) were lower in smokers when compared to controls. H. influenzae was detected in 65% of smokers and 20% of controls, whereas S. pneumoniae was detected in 57.5% of smokers and 12.5% of controls. M. catarrhalis was detected 5% in only smokers. After sequencing, the identified virulent H. influenzae strain SC50876 was found in smokers. Through the application of multiple regression analysis, it was found that there are significant negative correlations between H. influenzae and both FVC and PEFR in individuals who smoke. This study provides novel evidence that smoking impairs lung function and promotes early colonization of the lower respiratory tract by Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis, particularly the virulent H. influenzae strain SC50876. Multiple regression analysis revealed a significant negative association between bacterial presence and FVC and PEFR in asymptomatic smokers, suggesting that such colonization may accelerate functional decline and contribute to the early development of respiratory disease in otherwise asymptomatic individuals.