Objective To investigate the effect of different samples between swabs and bronchotracho alveolar larvage by real-time PCR in patients with community acquired pneumonia. Methods Clinical data, including 450 patients with severe pulmonary infection, samples of swabs and bronchotracho alveolar larvage were detected by real-time PCR. Results 115 patients were diagnosed with MPP (25.6%) in 450 patients of severe pulmonary infection. The positive rates were 69.56% and 13.04% in samples of BALF and swab, respectively. MP infection were frequent between patients aged 20-29 and 50-59 years. The big numbers of patient were most in age 50-59 years. Conclusion Mp remains one of the major pathogens in pulmonary infection. The positive rate of BALF detection is higher than that of swabs detection. The method of real-time PCR is effective means of diagnosis MPP.