First report on removal of Chattonella marina by natural magnetic sphalerite (NMS). NMS (1–2 g/L) could remove C. marina rapidly and efficiently. Temperature > 25 °C, salinity > 30 ppt and pH value < 7.5 enhanced algal removal. Adsorption and physical interaction lead to cell morphology change and removal. NMS exhibited excellent stability after magnetic recycling and repeated use.