The objective of this work is to develop DNA-based methods for identification of Microcystis strains and for discrimination of toxic and non-toxic strains among Microcystis and other related blooming-forming cyanobacteria. Our studies include three parts: 1. Identification of genus Microcystis via NEST-PCR; 2. Differentiation of seven Microcystis strains by RAPD; and 3. Establishment of whole cells PCR in discriminating toxic and non-toxic cyanobacteria. In order to identify Microcystis strains, Microcystis-specific PCR primers was designed according to the regions V6, V7, V8 of 16S rRNA. As illustrated by the NEST-PCR, all the Microcystis strains have the target amplification fragments, while the Aphanizomenon flos-aquae, Anabaena flos-aquae, Oscillatoria planctonica, Anabaena sp., Synechococcous elenpata show no aimed product. our results confirm the accuracy of the strains to be tested in the further research. In the second part of our study, randomly amplified polymorphic DNA PCR was used to get DNA profiles of 7 Microcystis strains. The genetic distance between Anabaena and Microcystis is over 0.68; whereas the values range from 0.073 to 0.507 among 7 strains of Microcystis. The results suggest that randomly amplified polymorphic DNA PCR is relatively reliable to infer genetic relation and evolution of Microcystis and is proved to be an alternative and complementary approach to the traditional methods to differentiate the Microcystis strains. The third part of our study aimed to answer: Do cyanobacteria in general possess peptide synthetase genes or is the presence of these genes limited to a few species? Is the occurrence of the mcy B gene limited to toxic Microcystis aeruginosa? meanwhile, we also aimed to develop a simple and sensitive protocol being table to set apart toxic and non-toxic strains in cyanobacteria, particularly in microcystis. Amplified with degenerate primers MTF/MTR, all the Microcystis strains and Aphanizomenon flos-aquae 44-1, Anabaena flos-aquae 1444 contain peptide synthetase genes, even when they are non-toxic. Oscillatoria planctonica 708 gave negative signal. Based on the evidence that Mcy B is closely related to microcystin biosynthesis, we have surveyed the distribution of the Mcy B gene in different cyanobacterial species. For this purpose, two primer pairs (Tox1P/1M; Tox2P/2M) were designed and specifically used to detect the mcy B gene. The primers were able to amplify fragments of the mcy B gene from DNA of all known microcystin producers; all the non-toxic strains being tested did not yield aimed PCR product. The result thus clearly demonstrated that it is quite possible to distinguish microcystin with non-microcystin peptide synthetases gene in the Microcystis using DNA techniques. To ensure the accuracy of the PCR, we checked the toxicity of all strain by HPLC, Mouse Bioassay and ELISA. All these methods test and verify the results of PCR. Furthermore, our study has created the 'Whole Cells PCR' protocol which has been proved to be a simpler and more sensitive method in discriminating the microcystin-producing and non-microcystin-producing Microcystis strains. The potential application of this protocol in monitoring and evaluating the natural waters samples has been emphasized and discussed in the light of our findings.