The subject of the paper is to study the effect of the different river habitat on biological diversity of microalgae in order to reveal the status of algae indicators in the evaluation of river ecosystem health. The study is conducted to compare planktonic algae and epilithic algae in Shendinghe rive (SR) and Qihe river (QR) of Danjiangkou reservoir in August 2010. The trophic status is evaluated by saprobic system. There are 193 species (varieties) belonging to 98 genera and 7 phylums of planktonic algae and 61 species (varieties) belonging to 36 genera and 3 phylums of epilithic algae in the samples of SR. There exist 165 species (varieties) belonging to 82 genera and 7 phylums of planktonic algae and 48 species (varieties) belonging to 10 genera and 4 phylums of epilithic algae in the samples of QR. 15 genera instructions 21 species (varieties) of saprobic indicators are identified in the monitored rivers. The number of oligonucleotide indicators in QR is higher than that in SR, and the number of eutrophication indicators in QR is lower than that in SR. The water quality of QR is Biologically superior to that of SR.