In the course of screening for biological active compounds from microbial origins, various strains were isolated from roots of Mimosa pudica using standard dilution agar plate method. One isolate was selected for further studies of bacterial anti-fungal properties. It was designated MSSP and identified as Burkholderia sp. by many biological characteristics such as carbohydrate utilization, biochemical and physiological test and 16S rDNA sequence homology search. To investigate antagonistic principle, anti-fungal compounds were extracted and fractionated by different solvent systems. An anti-fungal compound was isolated from its culture filtrate using organic solvent extraction, column chromatography and thin layer chromatography and pure solid form compound (MSSP2) was obtained. The chemical structure of anti-fungal compound was identified as 2-Hydroxymethyl-chroman-4-one based on the data obtained from spectroscopic analysis such as mass spectral analyses and NMR spectral data. The compound 2-Hydroxymethyl-chroman-4-one exhibited good activities against phytopathogen such as Pythium ultimum, Phytophthora capsici and Sclerotinia sclerotiorum.