Antibiotic resistance has become a global crisis in recent years, while wastewater treatment plants (WWTPs) have been identified as a significant source of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, commonly used disinfectants have been shown to be ineffective for the elimination of ARGs. With the goal of upgrading the conventional UV disinfection unit with stronger capability to combat ARB and ARGs, we developed a UV-assisted electrochemical oxidation (UV-EO) process that employs blue TiO2 nanotube arrays (BNTAs) as photoanodes. Inactivation of tetracycline- and sulfamethoxazole-resistant E. coli along with degradation of the corresponding plasmid coded genes (tetA and sul1) is measured by plate counting on selective agar and qPCR, respectively. In comparison with UV254 irradiation alone, enhanced ARB inactivation and ARG degradation is achieved by UV-EO. Chloride significantly promotes the inactivation efficiency due to the electrochemical production of free chlorine and the subsequent UV/chlorine photoreactions. The fluence-based first-order kinetic rate coefficients of UV-EO in Cl– are larger than those of UV254 irradiation alone by a factor of 2.1–2.3 and 1.3–1.8 for the long and short target genes, respectively. The mechanism of plasmid DNA damage by different radical species is further explored using gel electrophoresis and computational kinetic modeling. The process can effectively eliminate ARB and ARGs in latrine wastewater, though the kinetics were retarded.