Chlorine dioxide (ClO2) has been widely used as an effective disinfectant to control fungal contamination during postharvest crop storage. In this study, Fusarium oxysporum f. sp. batatas SP-f6 from the black rot symptom of sweetpotato was isolated and identified using phylogenetic analysis of elongation factor 1-α gene; we further examined the in vitro and in vivo inhibitory activities of ClO2 gas against the fungus. In the in vitro medium tests, fungal population was significantly inhibited upon increasing the concentration and exposure time. In in vivo tests, spore suspensions were drop-inoculated onto sweetpotato slices, followed by treatment using various ClO2 concentrations and treatment times to assess fungus-induced disease development in the slices. Lesion diameters decreased at the tested ClO2 concentrations over time. When sweetpotato roots were dip-inoculated in spore suspensions prior to treatment with 20 and 40 ppm of ClO2 for 0-60 min, fungal populations significantly decreased at the tested concentrations for 30-60 min. Taken together, these results showed that ClO2 gas can effectively inhibit fungal growth and disease development caused by F. oxysporum f. sp. batatas on sweetpotato. Therefore, ClO2 gas may be used as a sanitizer to control this fungus during postharvest storage of sweetpotato.