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Chemosynthetic ecosystems host unique geological, biogeochemical, microbial and faunistic settings, which provide key ecosystem services for human wellbeing. In the Argentine continental margin, the existence of chemosynthetic ecosystems is still unknown. We present the first finding of chemosynthetic ecosystems in the Argentine deep sea. We assessed and compared biological and geological settings for cold seeps at Malvinas Basin and Colorado Basin and a control site (no gas) at Colorado Basin. We found two cold seeps with crater-like geomorphic features (pockmarks) of 500-m and 1000-m diameter at depths of ⁓500 m. Both cold seeps exhibited methane gas bubbles trapped at the surface of the seafloor, one exhibited seepage into the water column. Cold seeps hosted dense benthic macroinvertebrates (≥300 μm) assemblages consisting mainly of polychaetes, peracarid crustaceans and mollusks. The fauna from Argentinean seeps exhibited δ13C and δ15N stable isotope signatures indicative of multiple trophic levels, supported by both chemosynthetic and photosynthetic sources of energy. The difference in bubbling to the water column was not associated with different trophic input of chemosynthetically-derived sources of energy, suggesting that gas input is mediated by the bubbles trapped in the seafloor sediments. The presence of gas bubbles trapped in the surface sediments of the ocean floor allowed the detection of ecological and trophic characteristics of active chemosynthetic ecosystems. Integration of the sub-bottom dimension can help improve our understanding of the interactions of chemosynthetic ecosystems with seafloor fluid flow in a more reliable manner than the gas plumes. These cold seeps host significant biodiversity and ecosystem functions of the deep ocean. They fall within areas tendered for oil and gas industry development, but have not been a focus of conservation efforts to date. Information provided here can inform effective conservation actions and improve our understanding of the distribution of chemosynthetic ecosystems worldwide.