Bacterial contamination compromises beneficial water uses, including domestic drinking water, in the Elk River watershed (Humboldt County, CA).  Land use in this watershed includes timber harvest, rural residences with septic systems, wildlife habitat, and limited beef cattle production.  Our objective was to develop a measure of  fecal contamination in Elk River from specific fecal sources including deer (Odocoileus hemionus columbianus), beef cattle (Bos taurus), or human (septic). Bacteroides, an anaerobic bacterium, has been demonstrated as an indicator of fecal contamination. It has limited survival and reproduction rates outside of the host and its detection in environmental samples can be an effective method for determining recent fecal contamination. DNA from a small tributary, deer feces and cattle feces was extracted with an Ultra Clean soil DNA isolation kit and amplified using general Bacteroides primers, Bac 32F and Bac 708R (Bernhard and Field 2000).  Environmental water samples from the Elk River yielded little DNA and did not amplify with these primers.  Bacteroides 16s DNA sequences from deer feces matched sequences for elk and exotic ruminants.  Amplified DNA extracted from the small tributary matched sequences for a wide variety of sources.  Human, bovine, and deer specific primers will be used to amplify DNA from fecal and water samples.