The fate of antibiotics and antibiotic resistance genes (ARGs) in constructed wetlands has received more concerns recently. This study aimed to assess the influence of hydraulic flow direction (down-flow or up flow) and substrate type (brick rubble or oyster shell) on removal of antibiotics and ARGs from swine wastewater. For antibiotic removal, all of treatments can remove more than 84% of oxytetracycline and difloxacin during two stages of operation. Brick-based columns had stronger antibiotic removal capacity due to properties of brick, including large porosity and micropore size and 32% of Fe2O3. The surface soils tended to adsorb much more oxytetracycline than difloxacin, as was opposite to brick and oyster shell. For ARGs removal, the removal efficiencies of tetracycline-resistance genes (tet) and integrase gene of Class 1 integrons ranged from 33.2 to 99.1%, without significant difference among treatments (p > 0.05). However, most of Sigma tet relative abundances in effluents of up-flow treatments were higher than those in influents, which indicated a risk to release relatively more antibiotic-resistant bacteria in proportion to total bacteria into environment. Significantly correlated with antibiotic concentrations, ARGs relative abundances in surface soils increased as the time progressed for all the treatments. Our results demonstrate that antibiotic removal using constructed wetlands is greatly affected by substrate type, whereas variation of ARG relative abundances in effluents and soils are determined by hydraulic flow direction. (C) 2016 Elsevier B.V. All rights reserved.