This study is concerned with investigating the antifungal effects of cement mortar with an organic antifungal agent on the Aspergilus niger which might be easily discovered in the interiors and exteriors of buildings. Two types of organic antifungal agents: isothiazoline/cabamate and nitrofuran, were used in this study for the purpose of investigating the antifungal effect of cement mortar with antifungal agent on the A. niger of various fungus which can be easily discovered in the interiors and exteriors of building. In addition to the investigation of the antifungal effect, the experiment of basic physical properties, such as compressive and flexural strengths, and flow test was carried out. Cement mortar with the antifungal agent of isothiazoline/cabamate exhibited the outstanding antifungal effects but the antifungal agent of nitrofuran did not give the antifungal effects to cement mortar. Although there is a very slight decrease in the strength, it is almost equal to that of cement mortar without antifungal agents.