Abstract:[Background] Brown rot on peach and nectarine trees caused by Monilinia spp. is an important fungal disease, and produces serious economic losses frequently in China. There may exist more than one species of peach brown rot pathogens. [Objective] To clarify the species and pathogenicity of brown rot pathogens from different peach-growing areas in China. [Methods] The pathogens were isolated from peach brown rot fruits of different peach production areas, using the method of single spore isolation. Identification and analysis of isolates were carried out by morphological characteristics, molecular biology methods, and inoculation assay. [Results] In this study 15 brown rot pathogen isolates were obtained from 8 different peach-growing areas. The morphological characteristics of the isolates were slightly different from each other, but the isolate hfyn from Yunnan Province was significantly different from the other isolates. Based on its morphology, rDNA ITS sequence and phylogenetic analysis, the isolate hfyn was identified as Monilia yunnanensis, which was a newly found brown rot pathogen, and the other 14 isolates were identified as Monilinia fructicola. PCR amplification using several pairs of specific primers confirmed the morphological and rDNA ITS identification results. Inoculation tests showed that the pathogenicities on peach fruits of 15 isolates from different peach producing areas were different. The isolates from Lishui, Zhejiang Province, Shijiazhuang, Hebei Province, and Qingdao, Shandong Province had more virulent, and the virulences of isolates from Kunming, Yunnan Province and Tai’an, Shandong Province were relatively weak. [Conclusion] The results indicated that the major pathogen of brown rot in peach-growing areas in China was Monilinia fructicola, and there were differences in morphology and pathogenicity among these isolates from different peach-growing areas. The result from the present study may provide a scientific basis for managing peach brown rot epidemics.