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Abstract The present study characterized the distribution and sources of polycyclic aromatic hydrocarbons (PAHs) in 57 sediment cores collected from estuary and tidal flat wetlands in the Bohai coast region and investigated the molecular degradation mechanism of PAHs. The results showed that the PAH concentrations in estuary sediments were significantly higher than in tidal flat sediments. PAH patterns and pollutant sources were more complicated in estuary sediments. Quantitative response relationships showed that in estuary sediments, the key factors affecting PAH degradation changed from initial dioxygenase genes and C23O to salicylate hydroxylase genes and C23O with an increase in the PAH ring number. In contrast, for tidal flat sediments, the initial dioxygenase genes remained the key factors (nidA and nahAc / nagAc , except only nidA for 5-ring PAHs) related to PAHs with different ring numbers. Non-metric multidimensional scaling (NMDS) analysis revealed that the lower catechol dioxygenase pathway coupled with the upper pyrene dioxygenase pathway. The total polycyclic aromatic hydrocarbon (TPAH) level across the Bohai coast region was most affected by catechol dioxygenation (catA + C23O). Catechol dioxygenation was directly affected by naphthalene dioxygenation/ nahG ((nahAc + nagAc)/ nahG), indicating that the interaction within the upper pathway coupled with the lower pathway. In addition, TOC had direct positive effects on catechol dioxygenation and nidA. This study improves our understanding of the biodegradative pathway of PAHs with different ring numbers and the response of PAHs to biotic and abiotic factors. Graphical abstract Image 1 Highlights • Initial dioxygenase genes were key factors for 2–6 ring PAHs in tidal flat sediments. • The lower pathway was dominant in the degradation of HMW PAHs in estuary sediments. • Lower catechol dioxygenase pathway coupled with upper pyrene dioxygenase pathway. • Catechol dioxygenation contributes to TPAH most and is directly affected in Bohai rim. [ABSTRACT FROM AUTHOR]