Biodegradation of organic compounds in groundwater can be a significant source of methane in contaminated sites. Methane might accumulate in indoor spaces posing a hazard. The increasing use of ethanol as a gasoline additive is a concern with respect to methane production since it is easily biodegraded and has a high oxygen demand, favoring the development of anaerobic conditions. This study evaluated the use of stable carbon isotopes to distinguish the methane origin between gasoline and ethanol biodegradation, and assessed the occurrence of methane in ethanol fuel contaminated sites. Two microcosm tests were performed under anaerobic conditions: one test using ethanol and the other using toluene as the sole carbon source. The isotopic tool was then applied to seven field sites known to be impacted by ethanol fuels. In the microcosm tests, it was verified that methane from ethanol (delta C-13 = -11.1 parts per thousand) is more enriched in C-13, with delta C-13 values ranging from -20 parts per thousand to -30 parts per thousand, while the methane from toluene (delta C-13 = -28.5 parts per thousand) had a carbon isotopic signature of -55 parts per thousand. The field samples had delta C-13 values varying over a wide range (-10 parts per thousand to -80 parts per thousand), and the delta C-13 values allowed the methane source to be clearly identified in five of the seven ethanol/gasoline sites. In the other two sites, methane appears to have been produced from both sources. Both gasoline and ethanol were sources of methane in potentially hazardous concentrations and methane could be produced from organic acids originating from ethanol along the groundwater flow system even after all the ethanol has been completed biodegraded.