We assessed variation in length, width, density, and surface enlargement factor of papillae; rumen and intestinal digesta weight; intestinal length; and intestinal tissue weight of reproductive and nonreproductive female white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) using similar burned and unburned habitat. Deer were collected from study areas in Custer and Pennington counties, South Dakota, in and adjacent to a wildfire burn. Length of papillae and enlargement factor of papillae surface of white-tailed deer and mule deer were greater in burned than unburned habitat, and dry weight of rumen digesta of white-tailed deer was greater in unburned than burned habitat. Papillae surface enlargement factor, papillae length and width, and dry weight of rumen and intestinal digesta were greater for lactating than nonlactating white-tailed deer. Papillae density, intestinal digesta dry weight, and intestinal length were greater in mule deer than white-tailed deer. The mosaic pattern of the burned habitat was beneficial at the mucosal level for white-tailed and mule deer within 3 years postfire. Enhanced papillae morphology of lactating compared with nonlactating and pregnant deer was attributed to high nutritional demands associated with reproductive status. Papillae density may be more important in mule deer because of feeding strategy (concentrate selector–intermediate feeder) compared to white-tailed deer (concentrate selector), whereas greater rumen digesta dry weight and intestinal length may be directly associated with size.