Objective To investigate the clinical features of lower respiratory tract infection caused by hypermastigote. Methods The clinical manifestations, chest imaging characteristics, fiber bronchoscopic and etiological test results were analyzed in 16 patients with hypermastigote infection in lower respiratory tract. Results In 16 patients with hypermastigote infection in lower respiratory tract, fever were present in all the cases, cough in 15 cases, night sweat in 12 cases, wheezing in 3 cases, and eosinophilia in 3 cases.Alive hypermastigotes were found in respiratory tract secretion in all the 16 cases. Bacterial culture of respiratory tract secretion yielded positive results in 8 of 16 cases. Chest imaging showed infiltrations in several lobes and segments or a large opacity with fuzzy patches. Bronchoscopy showed an acute inflammation in the respiratory tract lumen. Prognosis was good with the therapy of Metronidazole. Conclusions Detection of hypermastigote infection in lower respiratory tract have a definite clinical significance in Shenzhen area. Mixed infection is common in hypermastigote infection of lower respiratory tract.