A novel bacterium capable of producing a bluish-purple pigment was isolated from natural spring water. The bacterium was not capable of growth in soybean casein digest (SC) nutrient, but grew well in a ten-fold dilution of the SC nutrient medium. Based on 16S rRNA gene sequence analysis, the isolated bacterium was identified as being closely related to Duganella zoogloeoides. Ethanol extraction of the bluish-purple pigment revealed that the maximum absorbance of the pigment was at 576.5 nm. Based on the spectral characteristics, the main component of the pigment was predicted to be violacein. Production of the pigment required cultivation under oligotrophic conditions in a medium containing 0.5% NaCl at 25 °C. The pigment produced by the isolated bacterium exhibited antibiotic activity towards gram-positive bacteria (Bacillus subtilis), but not towards gram-negative bacteria (Escherichia coli). When tadpoles of Dryophytes japonicus were reared in water containing the isolated bacterium, a reduction in tadpole mortality was observed. These findings imply that the bacterium has a probiotic effect on the tadpoles of Dryophytes japonicus, by preventing fungal and bacterial diseases on the skin.