Abstract: Since 2013, there have been frequent outbreaks of filamentous algal blooms in Qinghai Lake from July to September every year. Blooms not only affect the growth of phytoplankton, but also adversely impact tourism. In this study, we collected bloom samples from Qinghai Lake and identified the species type. All specimens were observed with light microscope. The individual molecular phylogeny based on internal transcribed spacer (ITS) sequences and the concatenated molecular phylogenies based on small subunit ribosomal DNA (SSU), large subunit ribosomal DNA (LSU) were reconstructed. The results showed that these samples belonged to one Cladophora species. The species is closely related with Cladophora stimpsoniiand and Cladophora vagabunda, and belongs to the transition type from ocean to freshwater. Several characteristics can be used to distinguish it from similar Cladophora species: Plants live in brackish habitat, densely branched, slender and soft with typical intercalary and acropetal growth. Filaments, light green to bright green, have smaller cell-diameters. The cell diameter of main axes is about 30—90.0 μm with a L/D ratio of 2.4—8.0. The diameter of ultimate branches is 25.0—70.0 μm with a L/D ratio of 4.0—12.3. The diameter of apical cells is 25.0—50.0 μm with a L/D ratio of 3.6—12.0. On the basis of the morphological and phylogenetic analyses, we propose a new species, Cladophora qinghaiensis sp. nov.