The microbiome is known to influence the immune system. In humans, age-related dysbiosisand inflammation have been linked, but little is known in livestock.The aim of this study was to evaluate the digestive microbiota and its associations with ageand genetic background for mastitis.Forty Lacaune dairy ewes were included in the study, 20 ewes with ≥ 5 lactations (old) and 20ewes in first lactation (young). They were equally divided into two divergent lines selected formammary inflammatory response based on milk somatic cell count (SCC-, resistant andSCC+, susceptible to mastitis). Ewes were managed as a single group for several months atthe end of the lactation. After euthanasia, digestive content was sampled at different sites, andbacterial DNA was sequenced using the 16S rRNA gene. FROGS pipeline and mixOmicspackage were used for bioinformatics and statistical analysis.Based on the ruminal microbiota, “young” ewes can be distinguished from “old” ewes using ansPLS. Furthermore, within the “young” group, SCC- and SCC+ can be distinguished,whereas in the “old” subgroup, SCC- and SCC+ cannot be discriminated according to geneticline. In contrast, when the analysis was applied to faecal content, four distinct groups wereidentified.This study shows that the digestive microbiota of ewes varies with age and genetic backgroundfor disease susceptibility. Faeces might be a better matrix than rumen to discriminatemicrobiota changes about the predisposition to inflammatory responses.