Microorganisms with antagonist effects against the fungus Verticillium dahliae exist in the rhizospheres of grafted eggplants. Gas chromatography mass spectrometry (GC-MS) identifies both myristic acid and palmitic acid in the root exudates of grafted eggplants, which are absent in self-rooted controls; however, it is unknown whether these compounds affect microbes that are antagonistic towards V. dahliae. This study examined the allelopathic effects of myristic and palmitic acids on beneficial microbes and pathogens. We investigated the numbers of antagonistic fungi and bacteria and the numbers of microsclerotia of V. dahliae in rhizospheres of eggplants treated with myristic or palmitic acid. In addition, we examined the relationship between the antagonistic microbes and the V. dahliae in rhizospheres. Both myristic acid and palmitic acid were found to significantly increase colony-forming units (CFUs) of antagonistic fungi and bacteria, in a dose-dependent manner. However, these effects varied with stage. At lower concentrations of myristic acid, antagonistic microbes varied significantly at florescence. The effect of palmitic acid treatment was greatest at the fruiting stage. Moreover, increased concentrations of either compound correlated with a reduction of V. dahliae in the rhizosphere; again, the effects varied with stage. For example, the anti-fungal effect of myristic acid was most marked at florescence. In contrast, a low concentration of palmitic acid led to an increase in V. dahliae at florescence, but this effect was reversed at high concentrations. Moreover, a negative correlation was found between numbers of antagonistic microbes and V. dahliae in the rhizosphere. In the myristic acid treatment, the correlation coefficient was -0.8215 at the flower budding stage. Both the correlation coefficient and the determinative coefficient decreased concomitantly with eggplant growth stage. In the palmitic acid treatment, both coefficients displayed a parabolic trend:antagonistic microbe numbers increased concomitantly with a decrease in V. dahliae. The largest negative correlation occurred at florescence. This phenomenon may be due to stronger competitive effects of beneficial microorganisms. They first occupy colonization loci on the root to pathogenic bacteria nonviable in the rhizosphere. Therefore, it is likely that grafting alters the makeup of eggplant root exudates, which influence rhizosphere microbes and, in turn, affect the development of V. dahliae.