We have investigated the properties of films from polymer complexes obtained by the reaction of chitosan with poly(aminoproylethoxysiloxane) which are known to be constituted by molecularly compatibilized microdomains of the components. Specifically, we studied the influence that both, the acetylation degree the donor-acceptor activity of chitosan in the precursor solutions, have on the composition, thermal stability and morphology of the products. Comparison of the behaviour of two chitosans of similar molecular weight but different origin and acetylation degree, 12% and 17% respectively, shows that the latter is an important factor in stabilising the formation of chitosan aggregates in its solutions and films, thus making less efficient the formation of strong chitosan/polysiloxane interfaces. Dissolution of chitosan by microwave radiation improves polymer dissociation, thus increasing its donor-acceptor activity. That however also results, in this case, to disfavours strong hetero-polymer interfaces due to the large tendency of chitosan to self-aggregation.