The ecosystem defined as interaction between biotic components like plants, animals and microbes with abiotic components like air, water and mineral soil, in a specific and limited space. So, knowing diversity of cynobacteria will not only help in conserving using cyanobacteria itself but also give an idea about the other species accompanied with it and interact with it in the ecosystem. The work represented in this book focused on identifying diversity of cyanobacteria in the selected Egyptian protectorates which are not only differ in their aquatic habitat types i.e. marine, fresh water, brackish habitats but also geographically; identifying phylogenetic relationship of cyanobacterial isolates within protected areas under study and finally the geographical distribution range of cyanobacteria in the last ten years in Egypt.