Ficus altissima Bl. is a green plant distributed in tropics and subtropics with great ornamental value. A leaf spot disease is an critical disease in F. altissima, so it is important to prevent and control the disease when the pathogen is identified. A fungus is isolated from the diseased leaves, and is identified to be the pathogen of the disease. The pathogen is identified as Alternaria sp. after morphological observation. The internal transcriptional space (ITS) of rDNA, endopolygalacturonase (EPG) gene and the regions of OPA1-3 in genome of Alternaria are amplified and sequenced using direct colony PCR. The fungus is identified as A. gaisen based on both the sequences analysis and morphological observation.