The traditional way to identify algae is usually depend on the observation of the morphology. This way is time consuming and usually difficult to identify the algae during the early algal growth stage in which the character is not obvious and can not detect the subtle differences between species or strains; also, the morphology and the ability to produce toxicants of cyanobacteria may change under different natural or cultural conditions. In this paper, we use the molecular method to identify Anabaena species, the results showed that BSA are necessary for the PCR amplification and the optimal concentration is 1% (w/v) in the reacion buffer. DMSO increased or decreased the quantity of the amplification products selectively, but the effect is not significant. The self designed primers after comparison of other Anabaena PC sequences amplified the part of pcb and pca gene along with PC-IGS sequence when using both extracted DNA and pretreated whole cells as template, the banding pattern is not uniform but all produced the target bands, cloning and sequencing analyses indicated that PC in line with PC-IGS was amplified, even though the nucleotide between two Anabaena strains collected from two different regions in China show that only 2 sites in a fragment about 400 bp are different, but the PC-IGS sequences are quite different from others and thus can be applied to identify the different species or strains. The universal primers to amplify part of 16S rDNA and 23S rDNA along with their ITS sequence using the extracted DNA and pretreated whole cell showed that the banding pattern of amplification products are uniform when the whole cells were at the concentration of 105/mL in the reaction buffer, the minimum amount of whole cell to amplify the target band is 20 cells in 50muL reaction buffer.