Twelve cows and 14 goats were used to examine the differences between species in the rumen fermentation pattern and bacterial community structure when animals received the same diet. The balanced incomplete block design included 3 groups per species and 2 treatments (diets), differing in the composition of the concentrate: with corn as the main component (A diet) or with wheat plus sunflower oil (B diet). After 25 days of each of 2 periods, rumen fluid was collected using a stomach tube for microbial studies and pH, ammonia and volatile fatty acid (VFA) analysis. Differences in rumen fermentation due to species, diets and their interaction were observed, with greater ammonia concentrations and molar proportions of minor VFA, and lower percentages of acetate, in goats. Proportions of propionate and butyrate were higher in goats on the B and A diets, respectively. Several terminal restriction fragments (T-RF) also showed different relative frequencies due to species, diets and their interaction. Thus, some T-RF compatible with Prevotellaceae were more abundant in goats, whereas others that may correspond to Succinivibrionaceae were greater in cattle with the B diet. According to the percentages of dissimilarity between bacterial communities, the rumen ecosystem was affected alike by the diet consumed and the ruminant species