Current-year Fagus crenata seedlings survive damping-off in the forest-edge plot compared to those in the closed-stand plot. Greater illumination found in the forest-edge plot is likely to influence the defense of seedlings against pathogenic attack, by increasing the amount of phenolic compounds and forming periderm. This study aimed to clarify the chemical defense system by (i) isolation of antifungal compounds from seedling hypocotyls in the forest-edge plot, (ii) quantification of antifungal compounds in hypocotyls in the forest-edge and closed-stand plots, (iii) estimation of their antifungal activities against Cylindrocarpon sp. and Colletotrichum dematium and (iv) clarification of localization of phenolics in the hypocotyl tissues. Catechin and epicatechin were isolated as antifungal compounds showing inhibition of microconidia germination of Cylindrocarpon sp. and mycelial growth of Cylindrocarpon sp. and C. dematium. In the beginning of July when damping-off was the most severe in the closed-stand plot, the total amount of catechin and epicatechin in the forest-edge seedlings was approximately three times greater than that in the closed-stand seedlings. Flavan-3-ols, including catechin and epicatechin, were distributed mainly in the epidermal tissue on June 1 and in cortical tissues on June 15 and July 6, all from plants harvested from the forest-edge plot. We conclude that F. crenata could survive damping-off through chemical defense via catechin and epicatechin production and its distribution in seedling hypocotyls.