Previous paleoceanographic studies have used fossil foraminifera to assess the timing of ancient methane seepage. We examined modern analogs to determine the relationships between foraminifera and methane-influenced pore waters. Ambient pore water chemistry as well as vertical distributions and stable isotopic compositions of benthic foraminifera associated with methane seeps from the California Margin off Eel River and in Monterey Bay revealed faunal and geochemical differences between seeps. Carbon isotope signatures of living (rose Bengal stained) benthic foraminifera did not conform to the very negative (up to –58 per mil), methane-influenced carbon isotope values of the pore waters they live in. Instead, the influence of methane seep pore waters was reflected in the carbon isotopic variability of seep foraminifera, with substantial carbon isotope differences between individuals of the same species. For instance, delta ¹³C values of living Globobulimina pacifica varied by as much as 2.9 per mil between seeps within 50 km of each other, whereas delta ¹³C values of living Uvigerina peregrina varied by as much as 1.95 per mil within the same seep. Previous studies show that living U. peregrina typically varies by no more than 0.2-0.4 per mil within non-seep environments. Despite the large carbon isotopic variability within a species, the range of delta ¹³C values was generally within the reported range of values for these species in non-seep environments. Oxygen isotopic values of living seep foraminifera did not typically vary by more than 0.3 per mil. These results have important ramifications for studies of ancient methane seepage and climate change.