This study investigates the biodiversity of macrofauna inhabiting authigenic carbonate rocks at methane seeps on the Costa Rica margin. The research highlights the significant role of carbonate rocks in promoting macrofaunal diversity by providing unique habitats and food resources. The fauna found on these rocks are surprisingly similar to those in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary with seepage activity, biogenic habitat, and location. The macrofaunal community at non-seeping (inactive) sites is strongly related to the hydrography of overlying water, whereas the fauna at active seepage sites is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of certain polychaetes, whereas carbonates had more gastropods and other polychaetes. Stable isotope signatures and metrics showed that carbonate δ¹³C values ranged widely, and the food sources and nutrition used by the animals varied. The stable isotope signatures of carbonates and invertebrates were heterogeneous, with significant differences between active and inactive sites. Community metrics reflecting trophic diversity and species packing did not vary with seepage activity or site, but distinct isotopic signatures were observed among related, co-occurring species, reflecting intense microbial resource partitioning. The substrate and nutritional heterogeneity introduced by authigenic seep carbonates act to promote diverse, uniquely adapted assemblages, even after seepage ceases. The macrofauna in these ecosystems remain largely overlooked in most surveys, but are major contributors to biodiversity of chemosynthetic ecosystems and the deep sea in general.This study investigates the biodiversity of macrofauna inhabiting authigenic carbonate rocks at methane seeps on the Costa Rica margin. The research highlights the significant role of carbonate rocks in promoting macrofaunal diversity by providing unique habitats and food resources. The fauna found on these rocks are surprisingly similar to those in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary with seepage activity, biogenic habitat, and location. The macrofaunal community at non-seeping (inactive) sites is strongly related to the hydrography of overlying water, whereas the fauna at active seepage sites is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m). Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of certain polychaetes, whereas carbonates had more gastropods and other polychaetes. Stable isotope signatures and metrics showed that carbonate δ¹³C values ranged widely, and the food sources and nutrition used by the animals varied. The stable isotope signatures of carbonates and invertebrates were heterogeneous, with significant differences between active and inactive sites. Community metrics reflecting trophic diversity and species packing did not vary with seepage activity or site, but distinct isotopic signatures were observed among related, co-occurring species, reflecting intense microbial resource partitioning. The substrate and nutritional heterogeneity introduced by authigenic seep carbonates act to promote diverse, uniquely adapted assemblages, even after seepage ceases. The macrofauna in these ecosystems remain largely overlooked in most surveys, but are major contributors to biodiversity of chemosynthetic ecosystems and the deep sea in general.