Bingtang oranges with fruit spot were collected in Yuxi area of Yunnan province in 2017, the pathogens were isolated from typical lesions of Bingtang oranges. According to the morphological characteristics, pathogenicity and a variety of conservative gene sequence analysis, the pathogens were identified and the drugs against the pathogens were screened in the laboratory. The results showed that the isolated three strains guo-1,NS2-2 and NS2-6 belong to Phoma sp., which had strong pathogenicity to the leaves and fruits of the current year’s Bingtang orange; the phylogenetic analysis based on ITS, SSU, EF1-α, LSU, TUB and ACT showed that the pathogenic bacteria were in the same branch with Phoma sp.; the inhibition effect of 3% thiamycin wettable powder, 11.5% pyrazoxystrobin suspension, 22.5% prochloraz water emulsion and 60% dimefon water dispersible granule on the pathogen was obvious.