As part of our program to reconstruct the estuaries and lagoons history in Senegal and the diatom microflora inventory in Sene-Gambia, a 400 cm long core was taken at Ndangonkha in the Saloum estuary, near Foundiougne. The dating obtained show that sedimentation began in the Nouakchottian age, around 6000 years BP, with an average rate of sedimentation higher at the base than at the top where the high hydrodynamics of the environment would have caused sediment reworking. The comparative analysis of the lithology and the microflora shows a perfect correlation between the lutite fraction, the absolute abundance of diatoms and their specific diversity. The study allowed to inventory 110 species and varieties belonging to 62 genera; the most represented genera being Nitzschia (10 species), Coscinodiscus, Cyclotella and Diploneis (5 species each). Nine species are cited for the first time in Sene-Gambia. The microflora is dominated by euryhaline forms headed by Cyclotella striata. This dominance would be linked to the frequent variations in salinity between the rainy and dry seasons, while the abundance of marine species is related to the dominant influence of marine waters. The rare freshwater species encountered could be brought by wind, insects or birds. The analysis of the microfloristic and lithological data shows that the primary paleo-productivity and the specific diversity are weak at the base but increasing upwards (zone A), maximum in zone B whereas in zone C they are decreasing before disappearing in the last 10cm, in relation to the hydrodynamics of the environment.