We sequenced the transcriptome of the upside-down jellyfish Cassiopea xamachana during the establishment of symbiosis and strobilation. C. xamachana forms a symbiosis with the dinoflagellate Symbiodinium microadriaticum. While nutrient exchange is a key aspect of the symbiosis, the host requires successful infection by the symbiont in order to proceed through its life cycle. Approximately 2 to 3 weeks after infection, the scyphistomae will undergo strobilation. In order to determine the genetic mechanism behind the control of strobilation in Cassiopea, we compared host gene expression 3 and 8 days post-infection, as well as during the strobila stage.