Aims: The present study aimed to compare the microbiota composition from pigs fed different cereal grain types, either rye or triticale, as sole energy source. Methods and Results: Ileal digesta and faeces were sampled from eight pigs of each experiment. Illumina amplicon sequencing of the 16S rRNA gene was used to analyse the microbiota. Concentrations of short-chain fatty acids and ammonia were determined from faecal samples. The grain type revealed significant alterations in the overall microbiota structure. The rye-based diet was associated with an increased abundance of Lactobacillus in ileal digesta and Streptococcus in faeces and significantly higher concentrations of faecal short-chain fatty acids and ammonia compared to triticale. However, triticale significantly promoted the abundance of Streptococcus in ileal digesta and Clostridium sensu stricto in faeces. Conclusions: Diets based on rye or triticale affect varying intestinal microbiota, both of taxonomical and metabolic structure, with rye indicating an enhanced saccharolytic potential and triticale a more cellulolytic potential. Significance and Impact of the Study: Nutrient composition of rye and triticale are attractive for porcine nutrition. Both cereal grains show varying stimuli on the microbiota composition and microbial products of the ileum and faeces.