This study was conducted to isolate and identify the fungal pathogen causing seedling rot of Lithospermum erythrorhizon Siebold & Zuccarini, and to know the optimum growing temperature for decreasing seedling rot of Lithospermum erythrorhizon. On the basis of morphological characteristics, EF-1a sequence analysis, and pathogenecity to host plant, the fungi isolated from seedling rot and seeds of Lithospermum erythrorhizon were identified as Fusarium fujikuroi, indicating that disease causing fungus is seed-borne pathogen. Optimum temperature for germination of seeds of Lithospermum erythrorhizon was 15~20℃, but pathogenicity of Fusarium fujikuroi was shown more readily at 25~30℃. These results suggested that seedling culture of Lithospermum erythrorhizon between 15℃ and 20℃ might reduce seedling rot of Lithospermum erythrorhizon caused by seed-borne pathogen Fusarium fujikuroi.