Life history transitions are critical for many marine species and often correspond to concomitant developmental and ecological shifts between two contrasting environments: the ocean versus the reef or the coast. The metamorphosis of anemonefishes regulated by thyroid hormones (TH) perfectly illustrates such a connection between developmental and ecological shifts. Until recently, the nature of the changes occurring during this transition, if and how they are regulated by TH, and how the environment interacts with the TH system remained poorly investigated. Anemonefishes are becoming an emerging model in the field of eco-evo-devo (ecology, evolution, and developmental biology) allowing the investigation of the role of TH as an orchestrator of metamorphosis.