Cyanobacterial blooms cause extensive ecological damages in aquatic environments. Heterotrophic nanoflagellates (HNF) play an important role in controlling the populations of cyanobacteria in natural water bodies. In this study, we report a HNF, NF-WJ05, which grazes efficiently on the toxic cyanobacterium Microcystis aeruginosa strain PCC 7806. The morphological characteristics of the nanoflagellate observed by optical microscope and confocal microscope showed that NF-WJ05 could be a Paraphysomonas. The sequences of the internal transcribed spacer (ITS) regions of rDNA including the 5.8S rDNA region was determined and compared with sequences available in databases. The 5.8S rDNA sequence showed a high degree of similarity to those belonging to species of Chromophyta. However, sequences similar to that of its ITS were not found in the databases. Several environmental factors affecting the grazing efficiency of NF-WJ05 on cyanobacteria were evaluated. The more suitable conditions for grazing were 30°C and pH 5.0 with stirring. Ammonia inhibited the grazing, whereas low concentrations of phenol increased the grazing rate with an optimal concentration at 50 µg.L-1.