This chapter consists of two sections that discuss the possibility of using cyanobacteria to eliminate persistent organic pollutants (POPs) and to purify domestic wastewater. In the first section the biological purification ability of the cyanophytes Synechocystis salina and Phormidium foveolarum by cultivating them on the media with the addition of wastewater is discussed. The wastewater used in this study originated from the exit channel of the Biological Purification Station of Chisinau city, and was subsequently diluted as needed with distilled water. Cultivation media for the optimal growth of the Synechocystis salina species consisted of 20 % wastewater along with 10.9 mg/L of NH₄⁺, 0.11 mg/L of NO₃⁻, 0.01 mg/L of NO₂⁻, and 0.16 mg/L of PO₄³⁻. The media for the Phormidium foveolarum series was slightly different with a maximum of 10 % wastewater (7.9 mg/L of NH₄⁺, 0.05 mg/L of NO₃⁻, 0.12 mg/L of NO₂⁻, and 0.03 mg/L of PO₄³⁻). The concentrations of ammonium, nitrate, nitrite and phosphate ions were found to be largely reduced in 10–15 days after inoculation. Furthermore, these ions were not detectable in sediments and there was a comparable growth of the algal biomass, which thereby provides strong evidence that these ions were accumulated by cyanobacteria. The second section of this chapter presents data that details cyanobacteria’s capacity to degrade POPs. The organic pollutants, which are commonly used in industry and agriculture and are potential sources for degradation by cyanobacteria, include phenols, pesticides, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs). There is a considerable environmental benefit for the biodegradation of the persistent organic pollutants by cyanobacteria because they are not negatively affected by the process and can largely eliminate the presence of POPs. The most extensively studied cyanobacteria from this point of view are Anabaena and Nostoc genera. This chapter presents examples of using cyanobacteria to remove 2,4,6-trinitrotoluene, nitrophenol and p-nitrophenol, highly chlorinated aliphatic pesticides lindanes, organophosphorus compounds, phthalate esters, and DDT among others.