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Abstract Methane seeps occur at depths extending to over 7000 m along the world's continental margins, but there is little information about the infaunal communities inhabiting sediments of seeps deeper than 3000 m. Biological sampling was carried out off Unimak Island (3200–3300 m) and Kodiak Island (4500 m) on the Aleutian margin, Pacific Ocean and along the Florida Escarpment (3300 m) in the Gulf of Mexico to investigate the community structure and nutrition of macrofauna at these sites. We addressed whether there are characteristic infaunal communities common to the deep‐water seeps or to the specific habitats (clam beds, pogonophoran fields, and microbial mats) studied here, and ask how these differ from background communities or from shallow‐seep settings sampled previously. We also investigated, using stable isotopic signatures, the utilization of chemosynthetically fixed and methane‐derived organic matter by macrofauna from different regions and habitats. Within seep sites, macrofaunal densities were the greatest in the Florida microbial mats (20,961 ± 11,618 ind·m −2 ), the lowest in the Florida pogonophoran fields (926 ± 132 ind·m −2 ), and intermediate in the Unimak and Kodiak seep habitats. Seep macrofaunal densities differed from those in nearby non‐seep sediments only in Florida mat habitats, where a single, abundant species of hesionid polychaete comprised 70% of the macrofauna. Annelids were the dominant taxon (>60%) at all sites and habitats except in Florida background sediments (33%) and Unimak pogonophoran fields (27%). Macrofaunal diversity (H′) was lower at the Florida than the Alaska seeps, with a trend toward reduced richness in clam bed relative to pogonophoran field or non‐seep sediments. Community composition differences between seep and non‐seep sediments were evident in each region except for the Unimak margin, but pogonophoran and clam bed macrofaunal communities did not differ from one another in Alaska. Seep δ 13 C and δ 15 N signatures were lighter for seep than non‐seep macrofauna in all regions, indicating use of chemosynthetically derived carbon. The lightest δ 13 C values (average of species’ means) were observed at the Florida escarpment (−42.8‰). We estimated that on average animal tissues had up to 55% methane‐derived carbon in Florida mats, 31–44% in Florida clam beds and Kodiak clam beds and pogonophoran fields, and 9–23% in Unimak seep habitats. However, some taxa such as hesionid and capitellid polychaetes exhibited tremendous intraspecific δ 13 C variation (>30‰) between patch types. Overall we found few characteristic communities or features common to the three deep‐water seeps (>3000 m), but common properties across habitats (mat, clam bed, pogonophorans), independent of location or water depth. In general, macrofaunal densities were lower (except at Florida microbial mats), community structure was similar, and reliance on chemosynthesis was greater than observed in shallower seeps off California and Oregon.