Microcystis colonies are rich in polysaccharide materials which are the key factors influencing RNA extraction. In order to obtain high-quality total RNA from Microcystis colonies, comparative study of several methods including Method 1 PGTX-bead, Method 2 CTAB-bead, Method 3 FastRNA^® Pro Blue Kit and Method 4 RNeasy Mini Kit was conducted. All these methods were suitable for polysaccharide-rich materials. The integrity of RNA was analyzed by agarose gel electrophoresis, RNA concentration and purity were detected by Nanodrop ND1000 spectrophotometer, and DNA contamination was determined by qPCR. The results demonstrated that all the four methods were able to extract RNA from Microcystis colonies, and they were able to be used for downstream experiments, such as RT-PCR, after the contaminated DNA was removed. Method 1(PGTX-bead extraction) yielded RNA of highest concentration, good purity, low DNA contamination and it was low cost; Method 2 (CTAB-bead extraction) also yielded RNA of high concentration, but with heavy DNA contamination. This method was suitable for samples that need simultaneous isolation of RNA and DNA. Method 3 (FastRNA^® Pro Blue Kit)and Method 4 (RNeasy Mini Kit) extraction yielded RNA of low concentration, but Method 4 had simpler protocol, less time consuming, higher relative expression of the detected function gene, thus was suitable for extracting total RNA from small amount of Microcystis colonies.