Due to the emergence of virulent and antibiotic-resistant microbes, natural antimicrobials from herbal origins have been given more attention as an alternative therapy. This study provides an in vitro research framework to investigate the antibacterial activities of 5 herbal (marjoram, garlic, onion, cinnamon and black seed) oil extracts against 16 multidrug-resistant (MDR) and virulent P. multocida serogroup A isolates recovered from dead and clinically diseased rabbits. Pathogenicity of the screened isolates was further proven experimentally and was verified by PCR analyses of 5 randomly selected virulence genes encoding attachment and colonization proteins (ptfA, pfhA, and omp87), sialidases (nanB) and dermonecrotoxin (toxA). A total of 12 P. multocida isolates were highly pathogenic with the possession of all examined virulence genes, while the other 4 isolates were of lower pathogenicity with expression of the target genes except toxA. In vitro anti-P. multocida activities of the 5 extracts and their synergism rates with 4 antibiotic drugs revealed that marjoram and cinnamon extracts had the highest antibacterial activities and the highest synergism rates against the screened isolates. Pasteurella multocida virulence gene expression profiles were assessed via real-time quantitative reverse transcription PCR (qRT-PCR) in response to marjoram extract. The quantitative analyses showed less than five-fold reduction in the targeted virulence genes expression in presence of marjoram extract compared with the control. The findings from this study document a novel molecular inhibitory activity of marjoram against P. multocida multiple virulence genes and provide a proof of concept for its implementation as an alternative candidate for the treatment of pasteurellosis in farm animals in future.