[Objective] Identification of the pathogen of moldy-core disease of apple in Gansu Province. [Methods] The pathogenicity of fungal isolate was confirmed by Koch’s rule, and identification of the pathogen was performed according to anamorphic morphological characteristics and ITS rDNA sequence analysis result. [Results] A fungus isolated from moldy-core disease of apple in Tianshui County, Gansu Province, in January 2009. The fungus caused the same symptom compared to the natural mouldy-core disease while injected inoculation through the calyx tube of apple fruits. The fungus produced conidia with different morphological types: Conidia formed on acervuli (black conidiomata developed on mycelial mat in potato sucrose liquid medium after cultured 7 months at 3 °C?7 °C), (12.95 ?20.42) μm× (4.98?7.97) μm [av. (16.75±1.89) μm×(6.47±0.86) μm], 3 septa, rarely 4?5 septa, fusiform or ellipsoid, pale brown to brown, median two or upper three cells darker than the basal one, appendages laking; Conidia formed on mycelium (cultured 18 d on PSA plate at 10 °C), (12.45?59.76) μm×(4.98?11.21) μm [av. (30.10±11.16) μm×(7.26±1.28) μm], 2?9 septa, fusiform, clavate or worm-formed, initial slight colour, gradually altered to brown. [Conclusion] The fungus was identified as Discostroma fuscellum (Berk. & Broome) Huhndorf, based on anamorphic morphological characteristics and molecular identification (GenBank accession: JF320818). This is the first record of Discostroma fuscellum as the pathogen of apple moldy-core disease in China.