Fecal-borne microorganisms impact many shellfish-growing waters in coastal New Hampshire. Watersheds are often subject to fecal contamination by a variety of sources and efforts to improve water quality are often limited because of lack of information on which contaminant sources are most significant. Ribotyping and other microbial source tracking methods are useful new tools for providing information on the sources of fecal-borne bacterial contaminants in surface waters. New Hampshire has areas of abundant oyster (Crassostrea virginica) and clam (Mya arenaria) resources, the latter being most important in Hampton Harbor. In this study, Escherichia coli isolates (bacteria colonies) were obtained from water samples collected from ten sites in Hampton Harbor year-round during both dry and wet conditions. A library of known E. coli isolates was created from twenty different potential source species in the New Hampshire coastal watershed, including humans, livestock, pets, wildlife and avian species. The ribosomal RNA DNA of E. coli isolates was analyzed using ribotyping in which the patterns of ribosomal DNA were detected using chemiluminescence, then optimized and analyzed using GelCompar II software.