Many microalgae release polysaccharides, but the effects of the polysaccharides on mutual flocculation of microalgae and clay in aquatic environments have not been well studied. Aphanothece halophytica Frémy is a bloom-forming cyanobacterium in salterns and can release large amounts of polysaccharide (AH-RPS). In the present study, we investigated the effect of AH-RPS on mutual flocculation of cyanobacterium and clay and further explored the mechanisms by which AH-RPS affected mutual flocculation. We determined that AH-RPS possessed clay-dispersing activity as defined as the ability to inhibit the flocculation and sedimentation of clay suspensions in water. Supplementation of AH-RPS in cyanobacterial cell suspensions and in the culture media containing the same kaolin clay concentration dose dependently decreased flocculation of cyanobacterial cells and increased clay-dispersing activity. These findings indicate that the clay-dispersing activity of AH-RPS was related to its inhibitory effect on mutual flocculation of cyanobacterial cells and clay particles. Moreover, the clay-dispersing activity of AH-RPS was stable from pH 3 to pH 10 and was increased by adding NaCl, MgCl2, CaCl2, or low concentrations of KCl (up to 0.4 M). Taken together, our data suggest that AH-RPS might maintain its clay-dispersing activity and inhibit mutual flocculation of microalgae and suspended clay in saltern brine.