In the present study a new series of benzimidazole derivatives bearing various (benz)azolylthio moieties were synthesized so as to investigate their antimicrobial activity. Structures of the target compounds (5a-5i) were confirmed by their IR, H-1-NMR, ES-MS spectral data, and elemental analyses. The synthesized compounds (5a-5i) exhibited poor activity against bacterial strains. On the other hand, antifungal activity of the compounds against Candida species was very significant. Brine-Shrimp lethality assay was performed for determination of toxicity of the compounds. Compounds 5a, 5c, and 5d were evaluated as non-toxic in addition to their attractive antifungal activity. However, the other compounds (5b, e-i) in the series showed toxicity to different extents.