Essential oils from Chinese indigenous aromatic plants were tested for antimicrobial activity and induction of morphological changes in the tobacco pathogens Alternaria alternata, Colletotrichum destructivum and Phytophthora parasitica. The results revealed that the extent of mycelial growth inhibition was widely dependent upon the composition and concentration of essential oils. Among the 29 essential oils tested, superior broad‐spectrum antimicrobial activities were observed from cinnamon, geranium, cumin, thyme, basil and lemongrass essential oils. Concentration‐dependent inhibition was also determined for these active essential oils. The essential oils from cinnamon and thyme exhibited the strongest antimicrobial activity against mycelial growth of A. alternata, C. destructivum and P. parasitica. The essential oils also had a strong detrimental effect on spore germination of all the plant pathogens tested in a dose‐dependent manner. Compositions of the essential oils from cinnamon, geranium, cumin, thyme, basil and lemongrass were identified by gas chromatography and gas chromatography–mass spectrometry. The major components of these essential oils were cinnamaldehyde (80.4%), citronellol (41.6%), cuminaldehyde (46.9%), thymol (39.8%), linalool (50.0%) and citronellal (20.8%), respectively. Scanning electron microscopy revealed that these essential oils caused considerable morphological degeneration, including cytoplasmic coagulation, shrivelled hyphal aggregation, flattened empty hyphae, and swelling and lysis of hyphal wall in the three phytopathogens. Copyright © 2012 John Wiley & Sons, Ltd.