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The present study was conducted at 4 sampling sites of Lake Tanganyika and was intending to identify and estimate the spatial abundance of phytoplankton in relation to physico-chemical attributes. The species composition analysis of the samples has listed 115 species of phytoplanktons belonging to 7families from all sampling sites. The relative diversity index of families has indicated that Bacillariophyceae is the most dominant family in comparison to others families with 50 species (43.4%) followed by the family Chlorophyceae with 31 species (27%). The family Cyanophyceae was found very scarce with 3species (2.6%). Regarding quantitative data, the results of species richness and the Cumulative abundance of the sampling sites showed that phytoplankton species and density were variable among stations. Rumonge site holds first position with 115species which was the maximum of all species identified comprising 3450 individuals per liter followed by Kajaga site with 107species comprising 2482individuals per liter, then Mvugo site with 101species containing 1506individuals per liter and in the last position was Nyamugari site with 86 species comprising1031individuals per liter. Furthermore the results of Canonical Correlation Analysis (CCorA) between the environmental parameters and phytoplankton composition at sampling sites have shown that the abundance and proliferation of some phytoplankton species are negatively or positively affected by the physico-chemical parameters concentration because, some physico-chemical variables were found either inhibitors or accelerators for phytoplankton species growth.