Assembly of nanoparticles from bioactive peptides, caseinophosphopeptides (CPPs) and chitosan (CS) at physiological conditions and various CS/CPPs mass ratios have been systematically studied using a combination of turbidimetric titration, dynamic light scattering (DLS), electrophoretic mobility (zeta-potential) and transmission electron microscopy (TEM). Peptides, incorporated with CS forming nanoparticles, have already been prepared and identified using liquid chromatography-tandem mass spectrometry (LC-MS-MS). They are characteristic with different amount of clusters of phosphorylated seryl residues. At low salt concentration, an increase of CS/CPP mass ratio shifted the critical pHϕ1, which designated the formation of CS/CPP nanocomplexes, as well as pHmax, representing the neutralization of positive and negative charge to higher pH values. The peptide-polymer binding mechanism was analyzed according to the results of DLS, electrophoretic mobility, and TEM. First, negatively charged CPPs absorbed to positively charged CS molecular chain to form intrapolymer nanocomplexes saturated with CPPs (CPPNP). Then, the negatively charged CPPNP was bridged by added positively charged CS. Finally, novel nano-scaled spherical brushes were formed as additional CS molecule absorbed back to and bound the CPPNP. Phosphorylated groups in the CPPs might be the dominant sites for interaction with –NH3+ on the CS molecular chain.