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Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant (Orange hawkweed – Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy – Leucanthemum vulgare and Alsike clover – Trifolium hybridum) to determine if plant species hosted unique root microbiota. Our results show that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where gamma Proteobacteria and Acidobacteria occupied a larger portion of the community. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be explored.