Resistance to mercury is carried on mobile genetic elements that can be passed between members of a bacterial community. It was thought that the diversity of mercury resistance genes would increase with increasing mercury contamination and reflect a spatial distribution of sampling sites in a stream. Three sites along the stream were sampled in triplicate. DNA was extracted from these samples, PCR with fluorescent primers was used to amplify genes of interest and PCR products were digested with different restriction enzymes. Terminal restriction fragment length polymorphism analysis (TRFLP) was used to investigate the diversity and similarity of mer and 16S ribosomal genes from the three sample sites. Results indicate that choice of restriction enzyme, labeled end, and method of analysis affect the observed patterns. These results indicate that TRFLP can be used to compare patterns among genes, but the technique is limited when comparing results from different restriction enzymes.