Abstract: A series of halogen containing 1,4-naphthoquinon derivatives (1-4,5a-f) were synthesized and studied for their antifungal activities against C. albicans ATCC10231, C. albicans 955, T. mentagrophytes and M. gypseum. The results indicate that compound 2-hydroxy-3-chloro-1,4-naphthoquinone (2), 2-(N-acetyl)- acetamido-3-chloro- 1,4-napthoquinone (3) and 2-(N-acetyl)-acetamido-3-chloro- 1,4- napthoquinone (4) have potent antifungal activity. Among these promising antifungal candidates, 2 and 4 showed better activity than that of clinically antifungal drug clotrimazole (MIC = 8 μg/ml) with MIC = 1 μg/ml and 4 μg/ml, respectively against C.albicans ATCC10231. Compound 2 also exhibited an extremely potent activity (MIC = 0.25 μg/ml) against C.albicans 955 strain compared with clotrimazole (MIC = 16 μg/ml). Structure and activity relationship (SAR) study demonstrated that replacing of 3-position in 1,4- naphthoquinon by a Cl group is essential for antifungal activity. Meanwhile, antifungal activity was decreased considerably when the hydrogen atom at position-2 in naphthoquinone structure were replaced by a bulky group (e.g. diacetyl of phenyl group).