Microbes can initiate developmental gene regulatory cascade in animals. The molecular mechanisms underlying microbe-induced animal development and the evolutionary steps to integrate microbial signals into regulatory programs remain poorly understood. In the upside-down jellyfish Cassiopea xamachana, a dinoflagellate endosymbiont initiates the life stage transition from the sessile polyp to the sexual medusa. We found that metabolic products derived from symbiont carotenoids are important to initiate C. xamachana development in addition to conserved genes involved in medusa development of non-symbiotic jellyfish. We also revealed transcription factor COUP as a co-regulator of nuclear receptor RXR during metamorphosis. These data suggest relatively few steps may be necessary to integrate symbiont signals into gene regulatory networks and cements the role of the symbiont as a key trigger for life history transition in C. xamachana.