Significance Developmental plasticity is defined as the ability of an organism to adjust its development depending on environmental signals, thus producing alternative phenotypes precisely adjusted to the environment. Yet, the mechanisms underlying developmental plasticity are not fully understood. We found that juvenile clownfish delay the development of their white bars during metamorphosis depending on the sea anemone species in which they are recruited. To understand this developmental plasticity, we investigated roles for thyroid hormones, the main hormones triggering metamorphosis in vertebrates. We found that thyroid hormones regulate white bar formation and that a shift in hormone levels, associated with ecological differences, results in divergent color patterns in different sea anemone species in which the young fish is recruited.