An antagonistic Streptomyces strain was isolated from the shallow water sediment in Vizhinjam, Thiruvananthapuram coast. Based on the cultural and morphological characteristic studies, the strain was identified as new Streptomyces sp. Screening of secondary metabolites obtained from the selected strain led to the isolation of active fraction by using preparative TLC.The fraction was employed for the minimum inhibition (MIC) assay against seven clinical pathogens. Among these, Bacillus subtilis was found to be highly sensitive to the compound. Further the UV spectral analysis of active fraction revealed two absorption peaks, denoting the presence of active compounds of Polyene nature.