Significance Within the life span of an individual, animals adapt to their environment by adjusting their developmental programs dynamically. This phenotypic plasticity is highly specific to the lifestyle of an organism and represents a mechanism which may form the forefront of adaption to new environmental conditions. However, the implementation of the mechanism on the molecular level is not well understood. Here, we show that two taxonomic restricted or orphan genes are modulating the Wnt-signaling pathway in Hydra and that their expression depends on temperature and bacterial colonization. Our results demonstrate that environmental cues can be linked to developmental processes by the regulation of orphan genes that modulate conserved signaling pathways.