Culture-independent, molecular techniques were used to investigate the microbial community structure of an integrated constructed wetland (ICW) used for the treatment of agricultural wastewater. Procedures were optimised for total DNA recovery and polymerase chain reaction (PCR) amplification of 16S rRNA genes using archaea- and bacteria-specific oligonucleotide primers. Cloned PCR products were subsequently screened by amplified rDNA restriction analysis to identify operational taxonomic units (OTUs). Inserts from clones representing selected OTUs were sequenced and phytogenetic trees were prepared. A high Level of bacterial diversity was observed within the wetland, with the main species detected belonging to the Proteobacteria, the Gram Positive Bacteria and the Bacteroides-Flexibacter-Cytophaga group. Sequences closely related to organisms involved in the nitrogen (Nitrosomonas, Nitrospina sp.) and carbon (Methanosaeta sp., Methylobacter sp.) cycles were also detected, indicating the important role of microbes in nutrient cycling within wetland ecosystems.