The products of the microbial activity in the large intestine are an important source of energy for herbivores. A previous study showed differences in caecal methanogenesis and short-chain fatty acid (SCFA) profiles between brown hares and domestic rabbits. The present study was performed on animals which were offered the same diet to eliminate the impact of diet on the comparative analyses of microbial metabolites. Caecal samples of hares and rabbits were incubated in triplicate, i.e. without any supplementary substrate (control) or with the addition of wheat bran or oat bran. Calculated as percentage of body weight, the stomachs of the rabbits were heavier than those of the hares, but caeca of the hares weighed more than those of the rabbits. The total SCFA concentration in caecal samples was higher in rabbits than in hares, and it increased in both species when the supplementary fermentation substrates were added. In hares, the molar proportion of propionate was higher and that of butyrate was lower compared to rabbits. The addition of substrate decreased acetate and propionate but increased the molar proportion of butyrate. Microbial fermentation resulted in greater gas release in rabbit caecal samples compared to those of hares. Methanogenesis tended to be lower in hares than in rabbits, but high individual variability was observed, especially in hares. Our study stated lower microbial activity in the caeca of brown hares compared to domestic rabbits. The presented results might lead to assumption that differences between fermentation patterns were not caused by diet but resulted from the peculiarities of both species.