In order to address the diversity and structure characteristics of gut microbiota in the patients with asthma and study the relationship between gut microbiota and asthma disease, a case-control study involving 52 asthma patients and 25 controls were conducted. Total DNA was extracted from fecal samples using PCR-DGGE, and DNA fingerprints were obtained. Based on the DGGE profile, from 7 to 31 bands, average 17 are observed in asthma patients, while the corresponding values are from 14 to 36, average 24 in controls. The Shannon-Wiener diversity index is significantly lower in asthma patients than that in controls (P＜0.0001). Combining with the analysis by using multivariate statistical methods, it is indicated that two groups of samples are obviously classified by the structure of gut microbiota. However, the different between two nationalities and genders have no statistical significance. The gut microbiota of asthma patient proceeds remarkably changes at the molecular level, the diversity of gut micobiota decreases. The results suggest that there is a relationship between gut microbiota structure changes and asthma disease. Furthermore, PCR-DGGE combining with PCA and PLS-DA has the predictive and initiative advantages in the research of microbiota structure unknown samples. Therefore, the study could provide a means for the research and prevention of asthma.