To establish the relationship between polycyclic aromatic hydrocarbons (PAHs) and various stages of denitrification under denitrifying conditions in sediments, we examined the impact of PAHs on the vertical distribution of special denitrifying genes. In March of 2011, sediment samples were collected from three representative locations along the Pearl River. The characteristics of vertical distribution of PAHs as well as denitrifying genes in the sediment samples were analyzed. Based on these vertical characteristics, relationships between PAHs and special denitrifying genes (narG, nirS, nosZ and nrfA) were established using the multivariate method. Results of canonical correspondence analysis (CCA) showed a close correlation between high ring PAHs and dissimilatory nitrate reduction. The impact of PAHs on nosZ was the most significant, namely PAHs imposed strong inhibition on the nitrite reduction stage. Except for the nitrite reduction stage, denitrifying bacteria from other stages of denitrification acclimatized themselves to the high ring PAHs. Especially, bacteria containing nrfA may have the potential to anaerobically degrade high ring PAHs. Besides this, the special role of nirS remains to be studied further.