Urbanization leads to degradation in water quality and has a major effect on the biota of streams, but its effect on microbial communities is not as well understood. DNA-techniques that target functional genes are being used to examine microbial communities, but less frequently applied to freshwater aquatic systems. Our aim was to determine whether terminal restriction fragment length polymorphism and sequence analysis of polymerase chain reaction-amplified (PCR) nosZ gene sequences could be used to show if there were measurable differences in the denitrifying community in two urban streams in catchments with contrasting degrees of catchment urbanization. Community structure in the sediments and associated riparian zones were studied at the contrasting sites. We showed that the denitrifying community in the sediments and riparian soils of the two streams were significantly different. There were also significant differences between the sediment and riparian zone communities within each of the sites. Terminal restriction fragment length polymorphism analysis proved to be a valuable technique that could resolve patterns of the denitrifying community in streams of contrasting degrees of urbanization, but sequence analysis was required to confirm the identity of the amplified products.