Late Triassic and early Jurassic dikes and fissures in the Dachstein Limestone in the Northern Calcareous Alps harbor mass occurrences of the rhynchonellide brachiopods Sulcirostra juvavica and Halorella amphitoma. To test recent hypotheses about their paleoecology, we characterized these habitats using petrography, carbon stable isotopes, and trace element patterns, and found no evidence for hydrocarbon seepage or hydrothermal venting. Thus the brachiopods lived under normal-marine conditions, in darkness and absence of local photosynthetic primary production, hence relying on the supply of limited and presumably small-sized food washed into the dikes and fissures. Because Halorella and Sulcirostra occur in dikes and fissures since the beginning of their stratigraphic ranges, these rhynchonellides are not relics of formerly widely distributed taxa, but instead are two genera that rapidly adapted to these habitats. Both Halorella and Sulcirostra occur also in late Triassic and early Jurassic deep-water settings such as deep-marine sills and hydrocarbon seeps, indicating that close phylogenetic relationships between submarine cave faunas and deep-sea faunas, as seen today, existed also in the early Mesozoic, albeit among very different taxa. Another analogy to the modern cave fauna is the wide but disjunct geographic distribution of Sulcirostra and Halorella, both found throughout the Tethys and Panthalassa oceans. Our findings support the view that submarine cave habitats were continuously colonized by new taxa throughout Earth’s history.