Abstract: To understand the general situation of algae in source area of the Yellow River, an investigation on the phytoplankton assemblage was carried out in July (Summer) and October (Autumn) 2016. A total of 52 species of phytoplankton were identified, belonging to 7 phyla. Bacillariophyta and Chlorophyta were the main taxa, containing 21 species and 18 species respectively. Dominant species of phytoplankton were mostly oligotrophic or medium trophic species in diatom. Cell density of phytoplankton was low, only 6.90×104 cells/L~1.17×106 cells/L. Cell density in Summer was higher than that in Autumn, and cell density in lakes was higher than that in rivers. According to the assessment by cell density, Shannon-Wiener biodiversity index and Pielou evenness index of phytoplankton, the water quality in source area of the Yellow River were good, in extremely poor nutrition level or the poor nutrition level. The results can provide theoretical basis and data support for water ecological protection in source area of the Yellow River.