As cyanobacteria can be found in a wide variety of environments and can cause great damage to ecosystems, human health, and economy, it is important to monitor and understand their behaviour. In this case, the study aims to understand the spatial variations of cyanobacteria communities in the Gulf of Bothnia, by analysing environmental factors that affect them. I hypothesize that the variations from north to south and coast to offshore of nutrients such as phosphorus and nitrogen promote the occurrence of different cyanobacteria orders, i.e. Chroococcales, Oscillatoriales, and Nostocales. The methods used were 16S amplicon DNA sequencing and the traditional microscopy method. Both showed similar results: Nostocales seem to predominate south-offshore zones and Oscillatoriales coast-north stations. Nevertheless, contrary to what was hypothesized on the beginning, Chroococcales were widely distributed between the stations. Both analysis methods used have limitations and strengths, thus, they should complement each other. Moreover, the DNA method must be implemented in cyanobacterial monitoring for the Baltic Sea. On the other hand, it can be said that environmental variables such as nutrients, jointly with other parameters, such as salinity, pH, humic substances and DOC (dissolved organic carbon), influence cyanobacteria communities’ composition. Overall, the environmental factors in the Baltic Sea give cyanobacteria the perfect conditions for living and develop. Therefore, it is important to implement water management and monitoring plans, as temperatures are predicted to rise globally with climate change, thus, cyanobacterial blooms are also predicted to be more common.