Flocculation experiments were conducted with three kinds of polysaccharide-protamine complex flocculants. Alginate, κ-carrageenan, and pectin were used as typical polysaccharides. The polysaccharides have carboxyl and sulfate groups, and it can be considered that the polysaccharides could bind basic protein, such as protamine, at around the neutral pH (pH 6.5–7.5). The relative absorbance was used as an index of the flocculation efficiency. Influences of the mass ratio (polysaccharide/protamine) and dosage of the complex flocculants on the flocculation efficiency were investigated. Judging from the results, the optimum mass ratio of polysaccharide and protamine was found as 0.4 for alginate and 1.0 for κ-carrageenan and pectin. The previously proposed flocculation model was applied to the data successfully and the proportional constant, stoichiometric coefficients, and the equilibrium adsorption constant regarding as forming flocs were determined by fitting to the data and using a least square method. Judging from the model parameters, the total number of acidic groups, and the molecular weight of each polysaccharide, the alginate-protamine complex could be the most effective flocculant.