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Though therapeutic compounds can be extracted directly from medicinal plant tissues; it is now known that many phytotherapeutic compounds are actually produced by associated microorganisms or due to their interaction with the plant. Bouvardia ternifolia is a medicinal plant that can be considered a potential source of therapeutic compounds, such as the antitumoral molecule bouvardin. We characterized the endophytic, endophytic+epiphyte and soil bacterial microbiota in the flower, leaves, stems and roots in specimens of this plant through 16S rDNA sequencing. We found that Proteobacteria followed by Actinobacteria were the most abundant bacteria phyla in this plant. On the other hand, the most representative genera living endophytically were Propionibacterium, Paraccocus, Lactobacillus, Kaistobacter, Methylobacterium and Erwinia. This study provides evidence of the composition and diversity of the bacterial communities present in soil and tissues of B. ternifolia which can be considered for subsequent analysis and understanding of the therapeutic compounds that give this species its medicinal properties.