A mass extinction of deep-sea benthic foraminifera has been documented globally, coeval with the negative carbon isotope excursion (CIE) at the Paleocene-Eocene boundary, which was probably caused by dissociation of methane hydrate. A detailed record of benthic foraminiferal faunal change over approximately 30 k.y. across the carbon isotopic excursion at Ocean Drilling Program Site 690 (Southern Ocean) shows that shortly before the CIE absolute benthic foraminiferal abundance at that site started to increase. "Doomed species" began to decrease in abundance at the CIE, and became smaller and more thin-walled. The main phase of extinction postdated the CIE by a few thousand years. After the extinction faunas were dominated by small species, which resemble opportunistic taxa under high-productivity regions in the present oceans. Calcareous nannofossils (primary producers), however, show a transition to more oligotrophic nannofloras exactly where the benthic faunas show the opposite. Plankton and benthos is thus decoupled. Possibly, a larger fraction of food particles reached the seafloor after the CIE, so that food for benthos increased although productivity declined. Enhanced organic preservation might have resulted from low-oxygen conditions caused by oxidation of methane. Alternatively, and speculatively, there was a food-source at the ocean-floor. Benthic foraminifera dominating the post-extinction fauna resemble living species that symbiotically use chemosynthetic bacteria at cold seeps. During increased, diffuse methane escape from hydrates, sulfate-reducing bacteria could have produced sulfide used by chemosynthetic bacteria, which in turn were used by the benthic foraminifera, causing extinction by a change in food supply.