From 2016 to 2018, tuber rot disease was observed in Gastrodia elata in Muju and Jinan, Korea. During harvest, black spots and white hyphae on soil surface were observed in the tubers of G. elata. Additionally, the G. elata stored at 5℃ low temperature presented water-soaking and dark brown rot on the tubers. The colonies on potato dextrose agar were pinkish or apricotish white and felted with cottony and aerial mycelia of length 35 mm after a week. The optimal temperature for hyphal growth was 25-30℃, and at 5℃ or 40℃, the mycelial growth was almost inhibited. The macroconidia were falcate to almost straight, thin-walled, and usually 2-3 septate. The microconidia were usually formed on the monophialides of the hyphae and were hyaline, smooth, oval to ellipsoidal, and were almost aseptate or medianly 1-septate or occasionally 2-septate, and slightly constricted at the septa, and size were 3-15 μm × 3-6 μm. Based on the morphological characteristics and phylogenetic analyses of two molecular markers, internal transcribed spacer rDNA and translation elongation factor 1α, the fungi were identified as Fusarium oxysporum and Fusarium solani. Pathogenicity of a representative isolate was proved by artificial inoculation, fulfilling Koch’s postulates. To the best of our knowledge, this is the first report on tuber rot in G. elata caused by F. oxysporum and F. solani in Korea.