It is known that the rumen microbiome directly or indirectly contributes to animal production, and may be a prospective target for mitigation of greenhouse gas emissions [1]. At the same time, feed types and components of diet can influence the composition of the rumen microbiome [2,3]. Fluctuations in the composition of the digestive tract microbiota can alter the development, health, and productivity of cattle [4]. Many studies of cattle microbiomes have focussed on the rumen microbiota, whereas the faecal microbiota has received less attention [5], [6], [7]. Therefore, the features of the faecal and the ruminal microbiomes in different cattle breeds are yet to be studied. Here, we provided 16S rRNA gene amplicon data of the ruminal and the faecal microbiomes from Yakutian and Kalmyk cattle living in the Republic of Sakha, Yakutia, Russia. Total DNA was extracted from 13 faecal and 13 ruminal samples, and DNA libraries were prepared and sequenced on an Illumina MiSeq platform. Paired-end raw reads were processed, and final operational taxonomic units (OTUs) were assigned to the respective prokaryotic taxa using the RDP (Ribosomal Database Project) database. Analysis of the microbiome composition at the phylum level revealed very similar faecal microbiota between the introduced Kalmyk breed and the indigenous Yakutian breed, whereas the ruminal microbiomes of these breeds differed substantially in terms of relative abundance of some prokaryotic phyla. We believe that the data obtained may provide new insights into the dynamics of the ruminal and the faecal microbiota of cattle as well as disclose breed-specific features of ruminal microbiomes. Besides, these data will contribute to our understanding of the ruminal microbiome structure and function, and might be useful for the management of cattle feeding and ruminal methane production.