Introduction: Cyanobacteria are aquatic microorganisms that colonize a wide variety of ecosystems. Some produce secondary metabolites with pharmacological activities while some produce toxins harmful to human and animal health. Because of this dual interest, the issue of Cyanobacteria is the subject of much work worldwide. In this context, this study is carried out on the Aghien Lagoon (Cote d'Ivoire) in order to evaluate the photosynthetic activity and analyze the spatial distribution of Cyanobacteria. Material and Methods: Samples were taken from June 2016 to March 2018 at six stations located on the Aghien Lagoon. Chlorophyll (a) present in the water was measured by monochromatic spectrophotometry. The identification of Cyanobacteria was carried out according to the technique of morphological keys of Cyanobacteria. Results: The results of this study revealed that the Aghien lagoon is the site of strong photosynthetic activity measurable by variable levels of Chlorophyll a. Also, the results showed that 12 genera of Cyanobacteria are present in the lagoon with producers of secondary metabolites. Stations 2 and 3 near the village of Akandjé were the stations that contained the greatest number of genera of Cyanobacteria. Conclusion: It emerges from this study that the Aghien lagoon contains several genera of Cyanobacteria with a spatio-dependent distribution. In addition, the genus Microcystis, potentially producing secondary metabolites, is the most widespread genus in this Lagoon.