The stoichiometric distributions of both positive amino groups and negative sulfate ions loaded in chitosan-fucoidan nanoparticles (CFNs) were predicted quantitatively by correlating the separate yields of loaded chitosan and fucoidan, and a proposed relative charge density model (case 1). In addition, those distributions of both positive amino groups and negative sulfate ions loaded in CFNs were obtained by deriving the expression of their loaded concentrations directly from the experimental data (case 2). Both the model-prediction and experimental derivations were remarkably consistent with each other except at pH 2. The discrepancy between cases 1 and 2 at pH 2 was explained by an increase in the sulfate group loading because of the most intensive electrostatic (specific ion) interactions at pH 2. The ratio of the CFN-free net charge density shielded by counter-ions in the solution entrapped in CFNs to their counter-ion-crosslinking charge density was suggested to be a quantitative criterion for determining the size distribution of CFNs. The formation of CFNs ranked according to size was predicted well and explained reasonably by the suggested criterion, considering both the ionic strength of the entrapped solution in CFNs and the nonspecific binding (interaction) of the positive amino groups among the chitosan molecules. Furthermore, the fraction of nonspecifically-bound positive amino groups causing hysteresis was quantified from the positive net charged amino groups per unit-mass CFN. Thus, its magnitude was predicted to have a strong correlation with the CFN-preparation conditions, such as pH and fucoidan to chitosan mass ratio. (C) 2015, The Society for Biotechnology, Japan. All rights reserved.