Lignin peroxidase (LiP), manganese peroxidase (MnP) from Phanerochaete chrysosporium and laccase from Pleurotus eryngii were separately used to degrade alkali wheat straw lignin (AL). In order to characterize the catalytic action of the different enzymes, the chemical structure and the hydrodynamic properties of treated lignin were analyzed by thioacidolysis-gas chromatography and molecular size exclusion chromatography. The results confirmed that only LiP was able to degrade guaiacyl (G) and syringyl (S) structures in non-phenolic methylated lignins. However, provided that some phenolic terminal structures are present, MnP and laccase were able to degrade the non-phenolic part of the polymer linked by β-O-4 alkyl aryl ether bonds. This suggested that the oxidative reactions catalyzed in alkali straw lignin could progress through bond cleavages generating phenoxy radicals. The molecular size distribution of both thioacidolysis products and the oxidized polymer showed that AL underwent condensation side-reactions regardless of the enzymic treatment, but only LiP oxidation led to the increase in the hydrodynamic volume of the recovered lignin. This indicated that modification by enzymes of bonding patterns in lignin is not always associated with alterations in the spatial network of the polymer.