Previous studies have revealed certain genetic control by the host over the microbiome composition, although in many species the host genetic link controlling microbial composition is yet unknown. This potential association is important in livestock to study all factors and interactions that rule the effect of the microbiome in complex traits. This report aims to study whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Data on 16S and 18S rRNA gene-based analysis of the rumen microbiome in 18 dairy cows from two different breeds (Holstein and Brown Swiss) were used. The effect of the genetic background of the animal (through the breed and Single Nucleotide Polymorphisms; SNP) on the relative abundance (RA) of archaea, bacteria and ciliates (with average relative abundance per breed >0.1%) was analysed using Bayesian statistics. In total, 13 genera were analysed for bacteria (5), archaea (1), and ciliates (7). All these bacteria and archaea genera showed association to the host genetic background both for breed and SNP markers, except RA for the genera Butyrivibrio and Ruminococcus that showed association with the SNP markers but not with the breed composition. Relative abundance of 57% (4/7) of ciliate analysed showed to be associated to the genetic background of the host. This host genetic link was observed in some genus of Trichostomatia family. For instance, the breed had a significant effect on Isotricha, Ophryoscolex and Polyplastron, and the SNP markers on Entodinium, Ophryoscolex and Polyplastron. In total, 77% (10/13) of microbes analysed showed to be associated to the host genetic background (either by breed or SNP genotypes). Further, the results showed a significant association between DGAT1, ACSF3, AGPAT3 and STC2 genes with the relative abundance Prevotella genus with a false discovery rate lower than 15%. The results in this study support the hypothesis and provide some evidence that there exist a host genetic component in cattle that can partially regulate the composition of the microbiome.