This paper uses the method of 16SrRNA to analyze the microbial diversity in wetland wastewater treatment of Wuhan galaxy ecological agriculture Co., LTD . Using the method of 16SrRNA, we can get the molecular identification of the strain from screening , determine the 16SrRNA gene sequence and analyzes the homology of the corresponding sequence of related bacteria. The result shows that 32 strains are Bacillus subtilis, two strains are Bacillus licheniformis, six strains are Staptococcus cohnii, one strain is Staphylococcus epidermidis, one strain is Pseudomonas synxantha, and one strain is People umber bacillus in the first wetland. 36 strains are Bacillus subtilis, three strains are Bacillus licheniformis, one strains are Staptococcus cohnii, one strain is Proteus mirabilis, and two strain Staphylococcus epidermidis are the second wetland. The main strain in the two-stage wetland both are Bacillus subtilis.