Chitosan is a chitin-derived fiber, extracted from the shellfish shells, a by-product of the fish industry, or from fungi grown in bioreactors. In oenology, it is used for the control of Brettanomyces spp., for the prevention of ferric, copper, and protein casse and for clarification. The International Organisation of Vine and Wine established the exclusive utilization of fungal chitosan to avoid the eventuality of allergic reactions. This work focuses on the differences between two chitosan categories, fungal and animal chitosan, characterizing several samples in terms of chitin content and degree of deacetylation. In addition, different acids were used to dissolve chitosans, and their effect on viscosity and on the efficacy in wine clarification were observed. The results demonstrated that even if fungal and animal chitosans shared similar chemical properties (deacetylation degree and chitin content), they showed different viscosity depending on their molecular weight but also on the acid used to dissolve them. A significant difference was discovered on their fining properties, as animal chitosans showed a faster and greater sedimentation compared to the fungal ones, independently from the acid used for their dissolution. This suggests that physical–chemical differences in the molecular structure occur between the two chitosan categories and that this significantly affects their technologic (oenological) properties.