In this study, the effects of plants on the performance and bacterial community structure of palm mulch-based vertical flow constructed wetlands was studied. The wetlands were built in August 2013; one of them was planted with Canna indica and Xanthosoma sp., and the other one was not planted and used as a control. The experimental period started in September 2014 and finished in June 2015. The influent was domestic wastewater, and the average hydraulic surface loading was 208 L/m2d, and those of COD, BOD, and TSS were 77, 57, and 19 g/m2d, respectively. Although the bed without plants initially performed better, the first symptoms of clogging appeared in December 2014, and then, its performance started to fail. Afterwards, the wetland with plants provided better removals. The terminal restriction fragment length polymorphism (T-RFLP) analysis of Enterococci and Escherichia coli in the effluents suggests that a reduction in their biodiversity was caused by the presence of the plants. Thus, it can be concluded that the plants helped achieve better removals, delay clogging, and reduce Enterococci and E. coli biodiversity in the effluents.