[Objective] objectives of this study were to isolate and identify algicidal bacteria and scenedesmus, then analyze the inhibition mechanism on scenedesmus by algicidal bacteria. [Methods] Streak culture and physio-chemical properties were used to purify and identify algicidal bacteria respectively. The methods in “Microscopy and Chinese common freshwater planktonic algae” were used to isolate and characterize scenedesmus. The items including chlorophyll a, DO, scenedesmus cells, alga protein expression, special matter of algal inhibition were analyzed to clarify the influences of algicidal bacteria on scenedesmus. [Results] Four algicidal bacteria (R1?R4) were isolated and identified their genus of Bacillus sp. based on their physi-chemical properties. Algicidal bacteria R1 was proved for its most inhibition effects on scenedesmus. The inhibition of chlorophyll a was 65%; DO was 6.5 mg/L, far below to 10.4 mg/L obtained by the sole-culture of scenedesmus; The alga protein was only 0.192 6 mg/L and also far below to 0.845 7 mg/L of the normal alga protein expression without the inhibition of algicidal bacteria R1. FTIR results showed algicidal bacteria R1 could influence scenedesmus cell structure. The obvious inhibition of algicidal bacteria R1 on scenedesmus was also proved through phase contrast microscope during their co-culture process. [Conclusion] The inhibition mechanism of algicidal bacteria on scenedesmus including scenedesmus cell structure changes, scenedesmus protein and scenedesmus photosynthesis so on have been analyzed.