Abstract: An algicidal bacterium (FDHY-C3) with high-efficiency algicidal activity was isolated from the surface water of Changle coastal area, Fujian province. The morphological, physiological, biochemical and 16S rDNA sequence analysis was performed and the results indicated that the strain FDHY-C3 belongs to the genus of Alternaria. This strain showed a broad algicidal activity on diatoms, dinoflagellates and raphidophytes. The highest algicidal rate was detected on Skeletonema costatum, the algicidal rate can reach 98.18% in 72 h. The algicidal compounds was detected in extracellular secretions of FDHY-C3 cells through an indirectly dissolve way on target algal cells. The algal-lytic compounds of FDHY-C3 were not affected by freezing, but were affected by acidity and alkalinity and high temperature. The compounds can be extracted by ethanol and ethyl acetate, and was estimated to be protease. The molecular weight of this compound was between 10 kD and 14 kD.