Samples of leaf spot of Fagopyrum dibotrys (F. dibotrys) were collected from experimental base of Songming, Yunnan province, and the pathogen was isolated and cultured by tissue separation method. The pathogenicity of the pathogen was tested according to Koch’s rule. The pathogen was identified through morphological characteristics and phylogenetic analysis of ITS and TUB2 genes, and the biological characteristics of the pathogen was investigated. The results showed that the spore morphology of strain GY3, a representitive of the pathogen causing F. dibotrys leaf spot, was similar to the fungi of Pestalotiopsis. The rDNA-ITS and TUB2 sequences of strain GY3 was belonged to the branch which the rDNA-ITS and TUB2 sequences of two isolates (ZK1-1, ZK5-5) of Pestalotiopsis Microspora (P. microspora) belonged to, thus the pathogen causing leaf spot of F. dibotrys was identified as P. microspora. The optimum media for mycelia growth of strain GY3 was PDA. On PDA media, the optimum pH value for mycelia growth of strain GY3 was pH7, the optimum temperature for mycelia growth was 25 ℃ and the fatal temperature for mycelia was 50 ℃ for 10 min. Continuous illumination was favorable for mycelia growth and the optimum carbon source and nitrogen source for mycelia growth were glucose and peptone, respectively.