Abstract: Microcystins are a group of natural toxins known to be produced by certain types of freshwater blue-green algae and which have been shown to be liver toxins and tumour promoters, and pose a health hazard for humans, domestic animals and wildlife. The traditional methods for toxin extraction include 5% acetic acid, 75% methanol, 100% methanol, 70% acetonitrile and so on. The extracting solution using traditional methods should be firstly pass through a sep-pak cartridge, then was rinsed with water and 25% methanol in water, and then microcystins were eluted with 90% methanol water, which is very overelaborate and expensive. In this paper, a new rapid method for toxin extraction was provided based on boiling-water bath, and this method were used to extract cultures of five strains of colonial or single-celled Microcystis and one natural water bloom sample. With different times dealing in boiling-water bath, and through 0.45μm membrane, it was detected directly by HPLC-UV, and it was found that twelve minutes boiling-water bath was enough for microcystin extraction. Comparing with the traditional extraction methods, the comparative error of boiling-water bath extraction method was from 0.2% to 16.59%. The results illustrated that more time was needed for extracting toxins from colonial Microcystis than from single-celled one. This study provides an efficient, cheap and quick extracting method for microcystin, which reveals a comprehensive and applied prospect.