The microbial diversity of branches of Kaoping River at Lao-Nong Basin with altitudes from 100-2204m and Nantzuhien Basin with altitudes from 100-654m were studied. We used combining methods of bacterial, chemical and biotechnological to explore microbial diversity at the two basins to provide a reference for the environmental ecology of Kapoing River. It is the foundation for practicable environmental care. The results show the following: (1) The temperature in Tianchin at Lao-Nong Basin was lower(16.3¢J) than the rest of sampling sites(22-28¢J). (2) The temperature in Minsheng at Nantzuhsien Basin is lower(21.5¢J)than the of sampling sites(24-33¢J); other factors such as pH value, total organic carbon, and total organic nitrogen, varied according to different locations. In the microbacterial composition quantitatively, among all microorganisms, the bacteria content was the highest. Each gram of soil contain about 106~109 CFU at Lao-Nong Basin and 105~109 CFU at Nantzuhsien Basin, where as others such as the contents of actinomycetes and fungi were lower. Using 16s rDNA DGGE (denaturing gradient gel electrophoresis)analysis, the soil bacterial community composition at the two basin districts had discoverd that the microbial diversites at Nantzuhsine Basin were more abundant than those at Lao-Nong Basin. In regard to seasonal changes, our data agreed with traditional data. In the warm season, the microbial content is higher, and the community composition is also more abundant. The weather change in a short time period, such as a rainstorm and a quick shift of temperature seriously affected the number of bacteria. When the rain pours steadily down, it caused some degree of drop in bacteria number. However, when the rain stop, the microbacterial content and community composition gradually retured to original forms.