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Brown rot caused by the pathogen of the genus <i>Monilinia</i> is the most destructive disease in peaches worldwide. It has seriously reduced the economic value of the peach (<i>Prunus persica</i> (L.) Batsch) in Nyingchi and Qamdo, Tibet, China. <i>Monilinia fructicola</i>, <i>Monilia mumecola,</i> and <i>M. yunnanensis</i> have been reported as the causal agents of brown rot disease on stone fruits in China. In this study, we report on the identification of <i>M. yunnanensis</i> in peach orchards in Nyingchi and Qamdo, Tibet. From twenty-three isolates with the same characteristics, we identified the representative single-spore isolates T8-1, T8-8, and T8-20 as <i>M. yunnanensis</i> and confirmed that the Tibet brown rot disease was caused by <i>M. yunnanensis</i> based on the morphological characteristics and molecular analyses. The phylogenetic analysis of the glyceraldehyde-3-phosphate dehydrogenase (<i>G3PDH</i>) and β-tubulin (<i>TUB2</i>) nucleotide sequences and the multiplex PCR identification revealed that the representative isolates T8-1, T8-8, and T8-20 were more closely related to <i>M. yunnanensis</i> than other <i>Monilinia</i> species. Furthermore, the biocontrol strain of <i>Trichoderma</i> T6 presented significant antagonistic activity on the <i>M. yunnanensis</i> T8-1 isolate (T8-1) among the five <i>Trichoderma</i> strains. The highest inhibitory rates for <i>Trichoderma</i> T6 and its fermentation product against T8-1 mycelial growth were 72.13% and 68.25%, respectively. The obvious inhibition zone displayed on the colony interaction area between the colony of T8-1 isolate and <i>Trichoderma</i> T6 and the morphological characterization of the T8-1 hyphae were enlarged and malformed after inoculation with the <i>Trichoderma</i> T6 fermentation product at 20-fold dilution. Our results indicate that the strain of <i>Trichoderma</i> T6 could be considered as a beneficial biocontrol agent in managing brown rot of peach fruit disease.