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 $15{sim}20^{circ}C$, but pathogenicity of Fusarium fujikuroi was shown more readily at $25{sim}30^{circ}C$. These results suggested that seedling culture of Lithospermum erythrorhizon between $15^{circ}C$ and $20^{circ}C$ might reduce seedling rot of Lithospermum erythrorhizon caused by seed-borne pathogen Fusarium fujikuroi.