Different types of lignin were isolated from softwood (loblolly pine) and hardwoods with different S/G (syringyl and guaiacyl) ratio (eucalyptus and maple) via ball milling and dioxane extraction, and then reconstructed biomass was prepared by acid re-precipitation of isolated lignin onto bleached pulps. It was found for the isolated lignins that softwood lignin by itself adsorbed more cellulase than hardwood lignin. The carbohydrate conversion of physical mixture of bleached softwood and isolated lignin decreased to 81.4% from 90.3% when bleached softwood was used alone. When reconstructed biomass was tested, the carbohydrate conversion was further dropped to 64.6%, indicating a significant impact of physical blockage on substrate digestibility. Based on these observations, both non-specific adsorption and physical blockage are found important for the digestibility of lignocellulose. Effect of lignin structure (softwood/hardwood and S/G ratio) on digestibility will be discussed in terms of three inhibitory mechanisms suggested above.