Hydrothermal vent habitats are characterized by high hydrostatic pressure, darkness, and the continuous
release of toxic metal ions into the surrounding environment where sea anemones and other invertebrates
thrive. Nevertheless, the understanding of metazoan metal ion tolerances and environmental adaptations
remains limited. We assembled a chromosome-level genome for the vent sea anemone, Alvinactis idsseensis
sp. nov. Comparative genomic analyses revealed gene family expansions and gene innovations in A. idsseensis
sp. nov. as a response to high concentrations of metal ions. Impressively, the metal tolerance proteins MTPs is a
unique evolutionary response to the high concentrations of Fe²⁺ and Mn²⁺ present in the environments of these
anemones. We also found genes associated with high concentrations of polyunsaturated fatty acids that may
respond to high hydrostatic pressure and found sensory and circadian rhythm–regulated genes that were essential
for adaptations to darkness. Overall, our results provide insights into metazoan adaptation to metal ions,
high pressure, and darkness in hydrothermal vents.