The effects of phenanthrene (Phe) on the denitrification activity and denitrifying genes ( narG, nirS and nosZ) were evaluated by dose-response experiments in sediments of Dagu River Estuary (DRE) and Jiaozhou Bay (JZB). The results showed that potential denitrification activity (PDA), N 2O, NO 3 − and NO 2 − reduction rates of both areas were inhibited with an increase of Phe concentrations. The PDA, N 2O, NO 3 − and NO 2 − reduction rates of both areas was highest and lowest in the control (DRE: 0.453, 0.427, 7.439 and 3.222 mg N kg −1 h −1, JZB: 0.592, 0.555, 8.470 and 3.793 mg N kg −1 h −1) and highest Phe amended treatments (DRE: 0.069, 0.001, 4.486, and 1.563 mg N kg −1 h −1; JZB: 0.114, 0.024, 5.527 and 2.200 mg N kg −1 h −1). The inhibition rate of PDA was highest, follow by NO 2 − reduction and then NO 3 − reduction. Moreover, with the increasing of Phe concentrations, total bacteria count and the abundance of denitrifying genes were decreased. And N 2O accumulation was promoted with the addition of Phe for both areas. Based on the comparison of EC 50 values, denitrifiers harboring three genes were more sensitive to Phe than PDA, and denitrifiers harboring nirS gene were more sensitive, followed by nosZ gene, and then narG gene. Furthermore, according to correlation analysis, the relative abundance of denitrifying genes was much more positively correlated with PDA, NO 3 − and NO 2 − reduction than total bacteria count. In addition, the denitrification activity and total bacteria count in JZB were more inhibited than that of DRE. This study is useful for understanding the impact of Phe pollution on denitrification in estuary and marine sediments, with profound implications for the management of aquatic ecosystems regarding eutrophication (N-removal) and greenhouse effect.