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Antibiotic resistance genes (ARGs) and virulence genes (VGs) in wastewater treatment plants (WWTPs) may pose a potential threat to public health if without proper treatment. In this study, GeoChip was used to reveal the differences in ARG/VG diversity between a membrane bioreactor (MBR) and an oxidation ditch (OD) and the temporal co-occurrence patterns between ARGs and VGs. Results showed that the diversity of ARGs and VGs was lower in MBR than that in OD in the short term due to the better disinfection capability of MBR. However, the differences in diversity between two reactors disappeared in the long term because of the great variation of temperature. Instead, time-decay relationship was observed and overall turnover rate was −0.0105. Co-occurrence patterns indicate that direct connections between ARGs and VGs reduced sharply with time increasing due to the different responses of ARGs and VGs to environmental variation. Keywords: Antibiotic resistance genes (ARGs), Virulence genes (VGs), Wastewater treatment processes, Diversity, Temporal interactions