We examined the similarities and differences of the binding behavior of lysozyme (lys) with pectin varying in local charge density (blockwise distribution and statistical distribution of methoxyl groups, BP and SP) and similar degree of methoxylation (DM). The interaction at ionic strength I = 0.01 and pH 5.1 was found to be mainly electrostatic, associated with an exothermic enthalpy change. BP which is more inclined to self-association binds lys forming strongly associated complex particles with average sizes much larger (10–20 μm) than that of SP. The latter formed with lys small (0.6–3 μm) complex particles or liquid droplets depending on DM. The critical Iset and pHset values for BP/lys systems, above which complexes do not form, are not sensitive to DM (approximately 0.1 and 11.5 respectively), whereas for SP/lys systems the critical Iset and pHset values decrease significantly with increasing DM. The effect of I on complexation (CP) of lys with BP and SP has a nonmonotonic character. The distribution of BP and SP within the complex particles is irregular and is different for pectin with low and high DM values. The binding constant and stoichiometry ratio (lys/pectin) of the systems with SP are slightly higher than those of BP at the same DM, and these values decrease sharply (50 times) with increasing DM. The large positive changes in entropy in SP/lys systems suggest that the interactions in these systems tend to be more hydrophobic in character at high DM. On the other hand, with BP, a negative enthalpy change, especially for pectin with low charge, suggests the formation of a large quantity of hydrogen bonds or van der Waals interactions during CP.