A mass occurrence of the thyasirid bivalve Thyasira montanita in a limestone bed, exposed at Punta Montañita on the northern side of the Santa Elena peninsula in southeastern Ecuador, is here identified as an ancient methane-seep deposit. The massive to nodular limestone shows carbonate phases and microfabrics typical of seep limestones, such as banded and botryoidal cements. Its δ13 Ccarbonate values, as low as −52.6‰, suggest a biogenic methane source. Furthermore, the carbonate microfabrics and biomarkers typical of ANME-2 archaea indicate high seepage rates. Tubular fossils previously interpreted as worm tubes show cone-shaped projections and an internal structure consistent with that of crustacean cuticle and are here interpreted as crustacean fragments. Seep deposits with mass occurrences of thyasirid bivalves have so far only been reported from the Cretaceous, making the Montañita seep deposit the first such example from the Cenozoic. The faunal and biomarker inventories of this deposit indicate deposition on an open shelf; the oysters on the upper surface of the limestone are likely secondary encrusters that arrived only after the emergence of this deposit in shallower water.