Phytoplankton abundance in relation with physico-chemical parameters were investigated at 11 stations monthly from May 2014 to april 2015 in Aghien lagoon. Distribution of phytoplankton abundance had homogeny within the entire lagoon. However it notices differences between seasons. The high abundance was recorded in the low rainy season (2.3 107 cells/mL) and the low one in the high dry season (1.1 107 cells/mL).The seasonality is confirmed by Indicator value and RDA. Three groups were determined according seasons. The high rainy season assemblage was influence by conductivity and high temperature. Ammonium, BOD, dissolved oxygen and pH influence species of low dry season. Concerning the group 3 (high dry season and low rainy season), abundance of species is associated to high value of turbidity and nitrate. Indeed, the phytoplankton community of Aghien lagoon is still dominated by Cyanobacteria such as Microcystis wesenbergii (Komarek.) Komarek., M. aeruginosa (Kützing) Nägeli., Microcystis sp., Aphanocapsa incerta (Lemm.) Cronb. & Kom. and Anabaena circinalis Rabenh.ex Born. & Flash. These species are responsible for different blooms recorded in the Aghien lagoon. It also important to identified the kind of toxins these bloom-forming cyanobactorial produce in this lagoon.