Rhizoremediation is a strategy for recovering soils contaminated with polycyclic aromatic hydrocarbons (PAHs) based on the interaction of plants and microorganisms in soil pollutant removal. Secondary metabolites are components of root exudates of plants, which have been shown to have an effect on the microbial degradation of aromatic compounds in the rhizosphere. In this study, microorganisms capable of degrading anthracene and phenanthrene were isolated from the rhizosphere of Brassica nigra, and the effect of root exudates and plant secondary metabolites identified in the microbial degradation of PAHs was evaluated. The degradation percentages achieved when anthracene and phenanthrene were used as the sole source of carbon and energy were 35.1% ± 0.3% and 17.5% ± 5.1%, respectively. However, when glucose was added to the culture medium the percentage decreased to 24.8% ± 2.4% for anthracene and increased to 40.6% ± 3.6% for phenanthrene. In trials with root exudates, degradation percentages were 18.5% and 26.8% for anthracene and phenanthrene, respectively. In total, six secondary metabolites were identified in root exudates of B. nigra as follows: flavanone, flavone, Iso-flavanone, 7-hydroxyflavanone, 7-hydroxyflavone, and 6-hydroxyflavone. All had a negative effect on the degradation of anthracene except for 6-hydroxyflavone and 7-hydroxyflavanone. With phenanthrene, the most significant effect was obtained with glucose and 6-hydroxyflavone, which increased the degradation percentage to 51.8 ± 4.0. The results indicate that the composition of root exudates may affect microbial degradation and the effect of secondary metabolites, depending on PAH structure.