Abstract: ObjectiveEffects of different farmland applications on soil microbial community structure diversity in Jianhu wetland lakeside zone were studied to provide scientific references for appropriate utilization of wetland soil, and research and preservation of degraded wetland in Yunnan plateau. MethodAccording to crop distribution and types of different farmland applications in Jianhu wetland lakeside zone, soil samples were collected in five different farmlands (vegetable field, wheat field, broad bean field, oilseed rape field and lakeside zone) using square five sampling method. Total DNA of soil for different five sampling spots was extracted using Kit. Diversity index (H'), evenness index (J) and richness index (S) of bacterial com-munity structure were studied using PCR-DGGE technology. Physicochemical indexes viz., organic matter, total nitrogen and total phosphorus were measured using physicochemical property assay method.ResultThe results showed that soil samples of different applying farmlands had different Shannon-wiener diversity index, richness index and evenness index. Bacterial di-versity index, evenness index and richness index in wetland lakeside zone were higher than those in farmland soil. Bacterial community structure of wetland lakeside zone presented lower similarity to that of farmland soil, so it was clustered into a group alone. Bacterial community structure in different types of farmland soil shared high similarity (82%), so they were clustered into a group. Samples from the five collection spots were clustered into five groups at the similarity level of 93%. Mutual bands were found among different soil samples. Soil bacteria dominant species belonged to six categories, viz., Proteobacteria, Ox-alobacteraceae, Janthinobacterium, Duganella, Escherichia and Streptococcus.ConclusionSoil microbial community struc-ture diversity of different farmland in Jianhu wetland lakeside zone was abundant. Differences existed in soil physical and chemical properties, which affected the changes in soil microbial community structure and soil microbial diversity.