There is a growing need to mitigate the discharge of extracellular antibiotic resistance genes (ARGs) from municipal wastewater treatment systems. Here, molecularly-imprinted graphitic carbon nitride (MIP-C3N4) nanosheets were synthesized for selective photocatalytic degradation of a plasmid-encoded ARG (blaNDM-1, coding for multidrug resistance New Delhi metallo-β-lactamase-1) in secondary effluent. Molecular imprinting with guanine enhanced ARG adsorption, which improved the utilization of photogenerated oxidizing species to degrade blaNDM-1 rather than being scavenged by background nontarget constituents. Consequently, photocatalytic removal of blaNDM-1 in secondary effluent with MIP-C3N4 (k = 0.111 ± 0.028 min-1) was 37 times faster than with bare graphitic carbon nitride (k = 0.003 ± 0.001 min-1) under UVA irradiation (365 nm, 3.64 × 10-6 Einstein/L·s). MIP-C3N4 can efficiently catalyze the fragmentation of blaNDM-1, which decreased the potential for ARG repair by transformed bacteria. Molecular imprinting also changed the primary degradation pathway; electron holes (h+) were the predominant oxidizing species responsible for blaNDM-1 removal with MIP-C3N4 versus free radicals (i.e., ·OH and O2-) for coated but nonimprinted C3N4. Overall, MIP-C3N4 efficiently removed blaNDM-1 from secondary effluent, demonstrating the potential for molecular imprinting to enhance the selectivity and efficacy of photocatalytic processes to mitigate dissemination of antibiotic resistance from sewage treatment systems.