Background: The potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet whether gut microbiota participates in the development of hypertension remains largely unknown. To investigate this issue, we carried out comprehensive gut microbiota analysis and targeted metabolomics in a cohort of 29 non-treated hypertensive (HT) subjects and 32 normotensive (NT) controls. We assessed fecal microbiota composition by 16S rRNA gene sequencing and bacterial functions by metagenomic analysis. The microbial metabolites analysed were short chain fatty acids (SCFA) both in plasma and feces, and trimethylamine N-oxide (TMAO) in plasma.Results: The overall bacterial composition and the richness and diversity of bacterial community in the two groups were not significantly different. When the relative abundance of bacteria at OTU level was tested, Ruminococcaceae NK4A214, Ruminococcaceae_UCG-010, Christensenellaceae_R-7, Faecalibacterium prausnitzii and Roseburia hominis were found to be significantly enriched in NT group, whereas, Bacteroides coprocola Intestimonas and genera of Lachnospiraceae were increased in HT patients. We found a positive correlation between the HT-associated species and systolic blood pressure and diastolic blood pressure after adjusted for measured confounders. SCFA showed antagonistic results in plasma and feces, detecting in HT subjects significant higher levels in feces and lower levels in plasma compared to NT group. TMAO did not show significant differences between groups.Conclusions: Overall, our results present a disease classifier based on microbiota and bacterial metabolites to discriminate hypertensive individuals from NT controls in a first disease stage prior to drug treatment. HT subjects showed a particular SCFA profile in feces and plasma that could indicate a less efficient SCFA absorption in HT subjects.