[Background] Yunnan boasts abundant Cordyceps species resources and the natural Cordyceps species community contains diverse endophytic fungi, which can be used for mining antimicrobial.[Objective] To investigate the diversity of entomogenous fungi and the endophytic fungi in Dashao village, Songming county, Yunnan province, and screen strains with antimicrobial activities. [Methods] Entomogenous fungi and the endophytic fungi were isolated from Cordyceps species samples with tissue separation method. They were identified and the diversity was analyzed based on morphological observation and sequencing of ITS, nrSSU,nrLSU, tef-1α, rpb1, and rpb2. The activities against 7 pathogenic bacteria and 5 plant pathogenic fungi were tested by plate confrontation assay.[Results] A total of 86 natural Cordyceps species samples were collected, which belonged to 7 species in 5 genera in 3 families:Cordyceps (1 species), Beauveria (2 species), and Samsoniella(2 species) in Cordycipitaceae, Metapochonia (1 species) in Clavicipitaceae, and Ophiocordyceps (1 species) in Ophiocordycipitaceae. Meanwhile, 26 strains of endophytic fungi in 9 genera of 9 families were isolated from the samples, among which Trichoderma(38%) and Fusarium (19%) dominated. In addition, 20 strains, which were selected from entomogenous fungi and endophytic fungi according to their origins and taxonomy, were tested for the antimicrobial activities. Results demonstrated that 11 strains showed activities against two or more pathogenic bacteria, and 13 strains against more than one plant pathogenic fungi. Trichoderma sp. Y3-1 and Fusarium sp. WZ3-1 demonstrated broad-spectrum antimicrobial activities. [Conclusion] The Dashao village in Songming county of Yunnan province enjoys rich resources of entomogenous fungi and endophytic fungi and the isolated fungi show activities against diverse pathogens. This study enriches the diversity of entomogenous fungi in Yunnan province, providing not only data support for the development and utilization of entomogenous fungi and the endophytic fungi in Yunnan province but also strains for mining active substances from them.