The stable isotopic signatures of biophilic elements, such as carbon, nitrogen, and sulfur, exhibited in animal soft body parts are excellent indicators for evaluating the pathways of energy and food sources. Thioautotrophic and methanotrophic nutrition prevailed in deep-sea hydrothermal vent and methane seep areas results in sulfide-sulfur and methanecarbon isotopic ratios. In this study, we reevaluated the carbon, nitrogen, and sulfur isotope compositions of animals taken from deep-sea hydrothermal vents and methane seep areas in order to understand the detailed pathways of energy and food sources for the habitants. The results showed that most animals collected from sediment-starved hydrothermal areas rely on thioautotrophic nutrition, using hydrogen sulfide dissolved in venting fluids as the sole primary energy source. On the other hand, animals from sediment-covered hydrothermal vent and cold seep fields show some variations in energy sources, of both hydrothermal and microbial origins. Sediment-covered areas tend to be enriched in biomass and diversity relative to sediment-starved areas. The results suggest that fluid discharged through sediments to the seafloor are strongly affected by subsurface microbial processes and result in increased biomass and diversity of the seafloor animal community.