Mutualisms with chemosynthetic microbes are surprisingly rare in arthropods and their relatives. Despite the evolutionary benefit assumed in retaining symbionts through growth cycles, this molting group also lacks intracellular mutualisms. The current study provides evidence of the first chemosynthetic intracellular symbiosis in Arthropoda (Crustacea), discovered in extreme anchialine cave. These unusual groundwater systems enclose a landlocked marine layer, are typified by sharp salinity and oxygen gradients and are analogous to better studied extreme environments (hydrothermal vents, methane seeps). Our investigations via electron microscopy, stable isotope analysis and an enrichment experiment reveal that shrimp harbor endosymbiotic mutualistic bacteria. As intracellular mutualisms require more morphological and genetic adaptations than their extracellular counterparts, our findings shed light on the selective pressures towards endosymbiosis in extreme ecosystems. Intracellular symbiosis may serve as an innovation for maintenance of mutualistic bacteria through molt cycles in systems that are sparsely populated with low concentrations of chemosynthetic substrates.