This dataset provides the environmental data, species abundance and stable isotopes (δ13C, δ15N, and δ34S) of three faunal samples (PL604 C1, PL604 C2, PL602 C3) of Capelinhos hydrothermal structure (1,665 m depth, Lucky Strike vent field, Mid-Atlantic Ridge). The present dataset is provided as an Excel file (.xls) and includes 6 sheets: species abundances (Sp_abundance sheet), species stable isotopes (Sp_isotopes sheet), environmental variables (Env sheet), and temperatures associated to each sample (T_probe_PL604_C1, T_probe_PL604_C2, T_probe_PL602_C3 sheets). In 2014, we selected three close areas on the same Bathymodiolus azoricus mussel assemblage on a diffuse flow area at the base of the Capelinhos hydrothermal structure and deployed three temperature probes. The probes registered temperatures each 15 min for 9 months, from the 25th July 2014 to the 19th/22nd April 2015. In 2015, before faunal sampling, we measured in situ the sulfide (H2S) and iron (Fe(II)) concentrations using the chemical analyzer CHEMINI over the mussels. Then, we sampled fauna using the ROV Victor6000's arm (three to four grabs per sample) and placed it in isotherm boxes. Additionally, a suction sampler was used on each sampling area to clear the surface after grabs. We sieved samples through 250 µm and 20 µm mesh-sizes. The 250-µm samples were fixed in 96° ethanol directly. The 20-µm samples were preserved in formalin but are not showed in this dataset. We sorted individuals, and identified them to the lowest taxonomic level possible using stereo- and binocular microscopes. Only individuals with complete anterior regions were counted. We measured the carbon, nitrogen and sulfur isotopic ratios of 58 samples from 20 taxa. We used either muscle tissue fragments (for mussels and shrimps), whole specimens or pools of specimens for the other taxa. We manually removed hard carbonated parts (e.g., shells) to avoid bias due to the presence of inorganic carbon. We placed the gastropods Protolira valvatoides Warén & Bouchet, 1993 and Lepetodrilus atlanticus Warén & Bouchet, 2001) in tin cups and acidified their samples by directly adding HCl 1M, followed by 50 µl increments until no bubbling was detected. We performed isotope analyses at the University of Liège (Belgium) using a vario MICRO cube (Elementar, Germany) elemental analyzer coupled to an IsoPrime100 (Elementar, United Kingdom) isotope ratio mass spectrometer. We expressed isotope ratios using the δ notation (Coplen 2010), in ‰ and relative to the international references: Vienna Pee Dee Belemnite (carbon), Atmospheric Air (nitrogen) and Vienna Canyon Diablo Troilite (sulfur). IAEA (International Atomic Energy Agency, Vienna, Austria) certified reference materials sucrose (IAEA-C-6; δ13C = -10.8 ± 0.5‰; mean ± SD), ammonium sulphate (IAEA-N-1; δ15N = 0.4 ± 0.2‰; mean ± SD), and silver sulfide (IAEA-S-1 δ34S = -0.3‰) were used as primary analytical standards. Sulfanilic acid (Sigma-Aldrich; δ13C = -25.6 ± 0.4‰; δ15N = -0.13 ± 0.4‰; δ34S = 5.9 ± 0.5‰; means ± SD) was used as a secondary analytical standard. Standard deviations on multi-batch replicate measurements of secondary and internal lab standards (seabass muscle) interspersed with samples (one replicate of each standard every 15 analyses) were 0.2‰ for both δ13C and δ15N and 0.4‰ for δ34S.