Anarchic and galloping anthropization is degrading the hydro systems of coastal towns in Cameroon. Phytoplankton plays an important role in the maintaining of imbalance in these ecosystems. The aim of the study was to make a comparative analysis of phytoplankton diversity of the Tongo'o Bassa and Miana rivers with a view to propose measures to monitor these rivers for diversity conservation. Sampling took place monthly from March, 2020 to February, 2021. Phytoplankton was sampled in the pelagic zone of each watercourse. Total species richness of Miana river amounts to 10 classes divided into 41 genera and 46 species. Tongo'o Bassa river has 9 classes divided into 20 genera and 22 species. Shannon-Weaver Diversity Index is high to 3.21 bits to Miana river (station M3) and low to Tongo’o Bassa river of 1.35 bit (station T2). Class of Bacillariophyceae records the highest density at Miana river of 2400 ind/L obtained respectively to M1 and M3 stations. To the Tongo'o Bassa river, the densest class is Cyanophyceae with a maximum density of 4400 ind/L to station 2. Correspondence Factor Analysis (CFA) identifies 2 groups of species. Group 1 consists of 42 species, exclusive to Miana river. Group 2 consists of 15 species, exclusive to Tongo'o Bassa river. The phytoplankton diversity is poor in the Tongo’o Bassa river, very polluted area and rich in the Miana river, less polluted area. This analysis will be used to highlight a bio typology of phytoplankton population of these rivers from which management resources could be set up for a restoration of quality of Tongo'o Bassa river and a rational use of these resources rivers for sustainable development.