3,4-Dichloro-5-(6-chloro-9-(4-fluorobenzyl)-9H-purin-8-yl)isothiazole, a novel purine derivative, was synthesized by the cyclization of pyrimidine amine. Its structure was characterized by ¹H NMR, ¹³C NMR, ¹⁹F NMR, H RMS and single-crystal X-ray diffraction. This compound 3 is crystallized from a mixed solvent of dichloromethane and n-hexane (1:2, v/v) for structural identification as monoclinic crystal system, space group P2₁/n with a = 11.66250(10), b = 8.21300(10), c = 17.77920(10) Å, V = 1676.34(3) ų, Z = 4, D_c = 1.643 g/cm³, F(000) = 832.0 and μ = 6.301 mm^-1. 22315 reflections were measured (8.43≤2θ≤158.10°), of which 3532 were unique (R_int = 0.0311) and used in all calculations. The final R = 0.0334 (I > 2σ(I)) and wR = 0.0842 (reflections). The title compound showed over 50% of growth inhibition against Botrytis cinereal, Cercospora arachidicola, Gibberella zeae, Rhizoctonia solani and Sclerotinia sclerotiorum at 50 mg/L, and its EC₅₀ value against R. solani was 60.44 µmol/L, which was active at the same level as that of positive control diflumetorim with its EC₅₀ value of 60.29 µmol/L and less active than YZK-C22 with its EC₅₀ value of 12.32 µmol/L, respectively. Our studies discovered that the combination of bioactive substructures of isothiazole with purine could be an effective way to novel fungicide development.