A survey was undertaken from March to June 2014 on the biodiversity and the community structure of Chromista Cavalier-Smith, 1981 in Nyong and Kienke River mouths (South-Cameroon). In each river, raw waters were collected from upstream to downstream at four sites. Cells were counted using the Malassez cells procedure and species were identified. A total of 10427.1x10<sup>5</sup> cells corresponded to three phyla, eight classes, 23 orders, 32 genera and 40 species (24 freshwater species (60.0% of total species richness and total collection respectively), three marine species (7.5% and 2.4% of the total species richness; and total collection respectively), and one brackish water specialist in Kienke (2.5% and 5.1%), 13 tolerant species (32.5% and 32.6%)). The trophic diatom index revealed undisturbed conditions with no or little alteration of human origin and a low organic pollution (oligotrophic or mesotrophic state) (Nyong: TDI=52.7; Kienke: TDI=69.7; pooled assemblage: TDI=65.0). A low species richness was detected (richness ratio in Nyong: d=0.008; Kienke: d=0.003; pooled rivers: d=0.004), a high species diversity (Shannon index close to maximum) (Nyong: H’=2.742 and H’<sub>max</sub>=2.996; Kienke: H’=2.685 and H’<sub>max</sub>=2.996; pooled rivers: H’=3.245 and H’<sub>max</sub>=3.689), a very low dominance by a few species (Berger-Parker index close to 0) (Nyong: I<SUB>BP</SUB>=0.156; Kienke: I<SUB>BP</SUB>=0.175; pooled rivers: I<SUB>BP</SUB>=0.134), and Hill’s ratio were close to 1 (Nyong: Hill=0.819; Kienke: Hill=0.803; pooled rivers: Hill=0.722). The community was highly even with a high value of the Pielou’s evenness close to 1 (Nyong: J=0.915; Kienke: J=0.896; pooled rivers: J=0.880). Two useful species and one harmful species to fish were rare in Kienke. Species exhibited in Kienke and pooled data in rainy season, a positive global net association while it was negative in Nyong. Assemblage fitted Preston’s model in Nyong with a high environmental constant in the dry season (m’=1.469), low constant in the rainy season (m’=0.947) and the pooled seasons (m’=0.853). In Kienke constants were low (dry season: m’=0.574; rainy season: m’=0.566; pooled seasons: m’=0.581) suggesting a evolved community in less disturbed environments where the majority of species showed moderate abundances. In the dry season, the pooled assemblage functionned on the basis of maintaining a complex information network (close to ecological balance) developed at spatio-temporal scales (ZM model) and it presented a low force of regeneration (fractal dimension of the distribution of individuals among species (1/γ)=0.925<1). The evolved oligotrophic state (close to natural balance) of the chromists’ community should be preserved and protected and the studied rivers classified as reference.