Though phytoremediation has been widely used to restore various contaminated sites, it is still unclear how soil microbial communities respond microecologically to plants and pollutants during the process. In this paper, batch microcosms imitating in situ phytoremediation of petroleum-contaminated wetland by Scirpus triqueter were set up to monitor the influence of plant rhizosphere effect on soil microbes. Palmitic acid, one of the main root exudates of S. triqueter, was added to strengthen rhizosphere effect. Abundances of certain microbial subgroups were quantified by phospholipid fatty acid profiles. Results showed that diesel removal extents were significantly higher in the rhizosphere (57.6 +/-4.2-65.5 +/- 6.9%) than those in bulk soil (27.8 +/-6.5-36.3 +/- 3.2%). In addition, abundances of saturated, monounsaturated, and polyunsaturated fatty acids were significantly higher (P < 0.05) in planted soil than those in the bulk soil. When it was less than 15,000 mg diesel kg soil-1, increasing diesel concentration led to higher abundances of fungi, Gram-positive and Gram-negative bacteria. The addition of palmitic acid amplified the rhizosphere effect on soil microbial populations and diesel removal. Principal component analysis revealed that plant rhizosphere effect was the dominant factor affecting microbial structure. These results provided new insights into plant-microbe-pollutant coactions responsible for diesel degradation, and they were valuable to facilitate phytoremediation of diesel contamination in wetland habitats.