Leaf spots were observed on commercial plants of Bai Zhu (Atractylodes macrocephala Koidz.), a perennial herb that is used in traditional Chinese medicine in Panan County of Zhejiang Province, China. Approximately, 40% of the plants surveyed in the field showed severe symptoms of leaf spot during the summer of 2011. Fungal isolates obtained from infected leaf tissues were grown on Potato Dextrose Agar (PDA), and morphological characteristics of the colonies and the sporulating apparatus were determined. DNA extracted from the fungal culture was subjected to polymerase chain reaction (PCR) with primers ITS1F/ITS4 and Alt-for/Alt-rev, amplifying the internal transcribed spacer (ITS) regions and Alternaria allergen gene (Alt a 1 gene), respectively. The resulting PCR products were sequenced and compared for homology with other species in GenBank. Comparison of sequences of the Alt a 1 gene revealed 100% similarity with Alternaria longipes (Ellis & Everh.) E. W. Mason. Pathogenicity of the fungal isolate L 3 was confirmed on A. macrocephala. Taken together, we concluded that A. longipes was the causing agent for the leaf spot on A. macrocephala.