Faunal succession in whale-fall communities is closely associated with the progress of decomposition of the whale carcass. The main nutritional resources supporting a whale-fall community change from whale matter to chemosynthetic products over time. To study the geochemical aspects of this nutritional succession, we sampled animals over time on and in sediments around carcasses of sperm whale Physeter macrocephalus in Sagami Bay (mobile scavenger to early sulfophilic stage) and off Cape Nomamisaki (sulfophilic stage), Japan (500 and 200-300 m water depths, respectively). In these 2 areas, stable carbon, nitrogen, and sulfur isotopes of the animal soft tissues were measured to precisely elucidate the nutritional resources for each animal. In Sagami Bay, mobile scavengers relied only on whale soft tissue. Infaunal animals at 2 wk after the deployment relied only on whale soft tissue, while infauna at 9 mo after the deployment relied on chemosynthetic products. Such changes in nutritional resources were consistent with the transition of the geochemical environment in the sediments. Off Cape Nomamisaki, vigorous microbial sulfate reduction and thioautotrophic primary production nourished the fauna around the carcasses. The fauna in this area consisted of chemosymbiotic bivalves and necrophagous animals with sulfide-tolerant metabolism. We conclude that the changes in microbial processes, biomass, and compositions in sediments influence faunal succession in whale-fall ecosystems via change in the available nutrition for the fauna.