Symbiotic microorganisms are organized into specific ecosystems along the gastrointestinal tract of animals. In ruminants, studies showed a complex crosstalk between the ruminal microbiota and the host: beyond its role in the digestive process, the microbiota modulates the host phenotype but is also under the influence of the host genome. Concerning the intestinal microbiota, its role on numerous traits, in particular health maintenance, is increasingly described and could make it a key component of a sustainable breeding. However, its genetic control remains elusive. In this context, the present work will aim to perform a comprehensive genetic study of the lower gut microbiota. Faecal samples were collected between 2020 and 2022 from a population of 1930 Holstein cows, reared on 140 French commercial farms. Microbiota 16S rRNA analyses were performed on the samples and the data were processed to obtain amplicon sequence variant (ASV) tables. Genetic parameters were estimated using animal models for (1) the samples’ diversity expressed as the Shannon index, and (2) the abundance of the most frequently observed ASVs and genera (with a prevalence threshold of 60%). The 152 ASVs and 87 genera analysed showed low to moderate heritability estimates. Indeed, 32% of ASVs had a heritability between 0.05 and 0.23 (s.e. from 0.04 to 0.10), with an ASV of the Negativibacillus genus being the most heritable taxon. Almost half of the genera had heritabilities ranging from 0.05 to 0.21 while the Shannon diversity index appeared to be poorly heritable (h2=0.04, s.e.=0.05). Overall, our results demonstrate that the host genetics shapes the composition of the cow faecal microbiota. These first encouraging results will be complemented to assess the genetic correlations between the microbiota composition and production traits, and to identify genomic regions involved in the genetic determinism of the bovine gut microbiota through GWAS analyses.