Organic matter removal in a horizontal subsurface flow constructed wetland (HSSF) treating wastewater is associated with the presence of bacteria and archaea. These organisms perform anaerobic microbial processes such as methanogenesis, which can lead to methane emissions. The aim of this study was to evaluate methane production and characterize the bacterial and archaeal communities found in HSSFs treating secondary urban wastewater during cold and warm seasons. The pilot system used in this study corresponds to four HSSFs, two planted with Phragmites australis (HSSF-Phr) and two planted with Schoenoplectus californicus (HSSF-Sch), the monitoring was carried out for 1335 days. Removal efficiencies for organic matter (biological and chemical oxygen demand) and total and volatile suspended solids were evaluated in each HSSF. Moreover, biomass from each HSSF was sampled during warm and cold season, and methane productions determined by Specific Methanogenic Activity assays(maximum) (SMAm). In the same samples, the quantification and identification of bacteria and archaea were performed. The results showed that the degradation of organic matter (53-67% BOD5 and 51-62% COD) and suspended solids (85-93%) was not influenced by seasonal conditions or plant species. Potential methane production from HSSF-Sch was between 20 and 51% higher than from HSSF-Phr. Moreover, potential methane production during warm season was 3.4-42% higher than during cold season. The quantification of microorganisms in HSSFs, determined greater development of bacteria (38%) and archaea (50-57%) during the warm season. In addition, the species Schoenoplectus californicus has a larger number of bacteria (4-48%) and archaea (34-43%) than Phragmites australis. The identification of microorganisms evidenced the sequences associated with bacteria belong mainly to Firmicutes (42%), Proteobacteria (33%) and Bacteroidetes (25%). The archaea were represented primarily by Methanosarcinales, specifically Methanosaeta (75%) and Methanosarcina (16%). The community structure of the methanogenic archaea in HSSFs did not change throughout the seasons or plant species.