Five different chitosan samples (CHI-1 to CHI-5) from crustacean shells with high deacetylation degrees (>93%) have been deeply characterized from a chemical and physicochemical point of view in order to better understand the impact of some parameters on the bioactivity against two pathogens frequently encountered in vineyards, Plasmopara viticola and Botrytis cinerea. All the samples were analyzed by SEC-MALS, 1H-NMR, elemental analysis, XPS, FTIR, mass spectrometry, pyrolysis, and TGA and their antioxidant activities were measured (DPPH method). Molecular weights were in the order: CHI-4 and CHI-5 (MW >50 kDa) > CHI-3 > CHI-2 and CHI-1 (MW < 20 kDa). CHI-1, CHI-2 and CHI-3 are under their hydrochloride form, CHI-4 and CHI-5 are under their NH2 form, and CHI-3 contains a high amount of a chitosan calcium complex. CHI-2 and CHI-3 showed higher scavenging activity than others. The bioactivity against B. cinerea was molecular weight dependent with an IC50 for CHI-1 = CHI-2 (13 mg/L) ≤ CHI-3 (17 mg/L) < CHI-4 (75 mg/L) < CHI-5 (152 mg/L). The bioactivity on P. viticola zoospores was important, even at a very low concentration for all chitosans (no moving spores between 1 and 0.01 g/L). These results show that even at low concentrations and under hydrochloride form, chitosan could be a good alternative to pesticides.