This work aims to reveal the ecological status of the Porto-Novo Lagoon in the South-East of Benin, after some development works by analyzing phytoplankton communities. The phytoplankton sampling was carried out monthly from March to august 2017 using a plankton net (30 µm in diameter) at 6 sites located using a Global Positioning System (GPS). Alpha diversity was assessed using Shannon-Weiner index and Pielou evenness. The occurrence frequency of each taxon was determined for habitat preferences. The distribution profile of the taxa was revealed by a bio typology using the algorithm of Self Organizing Maps (SOM). In total, 160 taxa (genera and species) of phytoplankton belonging to 8 phytoplankton, 11 classes, 26 orders and 31 families have been identified. Cyanophyta, Eugenophyta, Dinophyta and Pyrrophyta were each represented by one class. It was the Chlorophyta with 4 classes followed by Diatomophyta, 3 classes that were the richest phyla. This observed biodiversity shows significant monthly variations. The highest densities of certain orders such as Cyanophyceae, Chlorophyceae and Euglenophyceae in the environment revealed the eutrophic state of the waters of the lagoon. The large number of accessory species, the different values of the various biodiversity indexes calculated added to the dominance of the various tolerant polluting species indicated the ecological instability of the lagoon despite the fitting up activities made in recent years. It is urgent to redefine the typical works to be done for the sustainability of this ecosystem.