Human microbiota may act as a reservoir for antibiotic resistance genes. Characterization of the human resistome is useful to understand the spread of antibiotic resistance. We aimed to identify naturally rifampicin resistant lineages that are among or phylogenetically related to the human microbiota. We obtained over 18000 bacterial reference genomes and extracted their rpoB gene encoding subunit beta of RNA polymerase. Translated rpoB sequences were then screened for the presence of single amino acid substitutions which were previously reported to confer phenotypic resistance to rifampicin in clinical/natural isolates as well as laboratory evolved mutants. Based on our results, certain rifampicin resistance mutations are present in most species belonging to Bifidobacteriales, Erysipelotrichales and Spirochaetia, many of which species are found in the human gastrointestinal tract. Moreover, predicted resistant species were distributed among the members of Clostridia (e.g. Oscillospiraceae, Clostridiaceae and Butyricicoccaceae), Flavobacteriaceae, Actinomycetes (e.g. Propionibacteriaceae and Microbacteriaceae), Mollicutes (e.g. Spiroplasmataceae, and Mycoplasmataceae), Proteobacteria and Lactobacillaceae (genus Weissella). Our study suggests that the human microbiota may be a rich source of intrinsic rifampicin resistant species.