Contaminant removal may largely be a function of many microbial processes in constructed wetlands. However, the role of microbial diversity for the removal of swine waste in constructed wetlands is limited. Here, we used 454/ GS-FLX pyrosequencing to assess archaeal, bacterial, and fungal composition within a surface flow constructed wetland to determine their spatial dynamics and contaminant removal within the wetland. We analyzed our data using UniFrac and principal coordinate analysis (PCoA) to compare community structure and specific functional groups of bacteria, archaea, and fungi in different sections of the wetland. PCoA analysis showed that, bacterial, archaeal, and fungal composition were significantly different (p=0.001) for the influent compared to the final effluent. Our results showed that, the wetland system contained relatively higher proportions of bacteria and fungi than archaea. Most of the bacteria and archaea that were associated with nitrogen removal were affiliated with Nitrosomonas which are ammonia oxidizing bacteria (AOB), Candidatus Solibacter, an anaerobic ammonia oxidizing bacteria (Anammox), as well as Nitrosopumilus, ammonia oxidizing archaea (AOA). The detection of AOB, Anammox, and AOA in this wetland shows abundance and diversity of these microorganisms that are responsible for nitrification processes in constructed wetlands.