A detailed monitoring of physic-chemical parameters and a complete inven-torization of phytoplankton species was conducted from May 2011 to May 2012 in Dakhla bay in south of Morocco. This study comes to bridge the gap of environmental data which has started since 2000 by Moroccan national institute of fisheries research (INRH) in this area. The results showed a differ-ence in the distribution of physic-chemical parameters (especially nutrient and dissolved oxygen). In addition, inventory of phytoplankton species has allowed identifying three different groups: diatoms (Rhizosolenia spp, Lepto-cylindrus spp, Thalassionema spp, Pseudo- nizschia spp.,...) represented 92% of the total phytoplankton flora, dinoflagellates (Scrippsiella sp, Prorocen-trum sp, Gymnodinium sp.,...) with 7%, while Silicoflagellates (Dictyocha sp) contributed with 1%. Seasonal fluctuation of these groups was governed, in first order, by the importance of upwelling in the region during the summer (intense phytoplankton activity). Yet this activity was much stronger in the PK25 site for tourism activity that suggested a remarkable anthropogenic input. An occurrence of Scrippsiella species (45% Hoja Iliamera growing area) and Prorocentrum sp (41% Duna Blanca aquaculture area), recognized as species of colored waters, was permanent at the study sites. Alexandrium sp represented 1% of the total dinoflagellates in Duna Blanca (<1% in the other sites), whereas Dinophysis sp (<1%) was observed in Lassarga (the entrance bay) and PK25 only. The latter two species are potentially the cause of PSP toxins's production (Paralytic Shellfish Poisoning) and DSP (Diarrheic Shellfish Poisoning) source of contamination of bivalves in the Bay during 2004 and 2006.
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