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Periodontitis and peri-implantitis are inflammatory conditions with a high global prevalence. Oral pathogens such as <i>Porphyromonas gingivalis</i> play a crucial role in the development of dysbiotic biofilms associated with both diseases. The aim of our study was to identify plant-derived substances which mainly inhibit the growth of “disease promoting bacteria”, by comparing the effect of <i>Rheum palmatum</i> root extract against <i>P. gingivalis</i> and the commensal species <i>Streptococcus oralis</i>. Antiplanktonic activity was determined by measuring optical density and metabolic activity. Antibiofilm activity was quantified using metabolic activity assays and live/dead fluorescence staining combined with confocal laser scanning microscopy. At concentrations of 3.9 mg/L, <i>R. palmatum</i> root extract selectively inhibited planktonic growth of the oral pathogen <i>P. gingivalis</i>, while not inhibiting growth of <i>S. oralis</i>. Selective effects also occurred in mature biofilms, as <i>P. gingivalis</i> was significantly more stressed and inhibited than <i>S. oralis</i>. Our studies show that low concentrations of <i>R. palmatum</i> root extract specifically inhibit <i>P. gingivalis</i> growth, and offer a promising approach for the development of a potential topical agent to prevent alterations in the microbiome due to overgrowth of pathogenic <i>P. gingivalis</i>.