The isotopic composition of the dissolved inorganic carbon (DIC) collected at sites of active methane discharge on Hydrate Ridge, Oregon, reveals anaerobic methane oxidation mediated by bacteria, with δ13CDIC reaching values as low as −48‰ in the upper 4 cm of the sediment. In spite of the high sulfide levels in the discharging fluids, living specimens of the benthic foraminifera Uvigerina peregrina are abundant in the vents, probably owing to the rich bacterial food source. Although pore water δ13CDIC is extremely low (−6 to −48‰), the δ13C values of living (Rose Bengal stained) foraminifera shells collected from active methane seeps are not significantly lower than those observed in nonventing pelagic sediments, and are within the range expected from local organic matter decomposition (0 to −4‰). The apparent δ13C disequilibrium between biogenic calcite and DIC suggests that at seep localities, foraminifera calcify mostly during periods when there is little methane discharge or during intermittent episodes of seawater flow into the sediments. The isotopic composition and Mg/Ca ratios of fossil (unstained) foraminifera recovered at carbonate-rich sites on the northern Hydrate Ridge reveals overprinting of the biogenic record by inorganic calcite with high Mg/Ca and anomalously low δ13C values. Thus overprinting of the original isotopic composition of foraminifera by overgrowths or recrystallization at or below the sediment surface, rather than primary calcification in contact with 13C depleted DIC, can explain extreme 13C depletion observed in fossil foraminifera recovered from sites of active methane discharge.