Abstract <p>The effectiveness of using chitosans with different characteristics (molecular weight, viscosity, and deacetylation degree) when harvesting the biomass of the cyanobacterium <i>Arthrospira platensis</i> by flocculation was assessed. It has been shown that the molecular weight of the polymer is the main characteristic influencing the process of biomass harvesting. The flocculation efficiency for all tested chitosan samples reached 90% within an hour of starting the process. When using chitosans with a molecular weight of 250 ± 50 kg/mol and a deacetylation degree of 65 ± 5% as a flocculant, it took less than five minutes to achieve a flocculation efficiency of 95%. From the biomass obtained as a result of flocculation, a one-stage extraction of phycobiliproteins, C-phycocyanin and allophycocyanin, was carried out. The use of chitosan during biomass harvesting did not affect the degree of extraction of phycobiliproteins, but increased the purity and antioxidant activity of the crude extract by 41–50 and 30%, respectively, relative to the control, depending on the characteristics of the chitosan. Thus, the use of the natural biopolymer chitosan in the flocculation process of a suspension of cyanobacterium <i>A. platensis</i> cells significantly reduces the time of biomass harvesting and increases the purity of crude phycobiliprotein extracts, which allows their use in the food and cosmetic industries, bypassing an additional stage of purification.</p>