The understanding of the human microbiome, especially of the oral cavity, has expanded exponentially since the advent of 16 rRNA PCR gene sequencing. Since the respiratory tract starts from the oral cavity and ends in the lung, study of the relationship between the oral microbiota and the lungs will allow us to understand the changes in lung disease compared with healthy state. The oral and lung microbiota were found to be similar, but the oral microbiota had greater diversity. The oral cavity especially the dorsal tongue was found to be a reservoir for bacteria causing pneumonia and chronic lung infection in cystic fibrosis. Oral and lung infections seem to all share the similar pathogenesis of oral microbiota dysbiosis. Certain oral bacteria were found to be potential biomarkers for lung cancer. Improvement in oral health is important especially in the management of lung diseases with infectious etiology. Oral microbiota can serve as biomarkers for diseases especially in lung cancer.