The Brachyury subfamily of transcription factors plays key roles in animal development, but their expression and function vary between taxa. Studies have shown that Brachyury specifies the mesoderm in vertebrates, while others suggested that it regulates blastopore and endoderm-ectoderm demarcation in some Cnidarian species (Hydra, corals, etc.). It also functions in the growth zone where terminal addition of serial elements such as segments is the ancestral condition in Bilateria. However, no study has been done to investigate its role in the formation of the free-swimming medusa stage of Medusozoa, such as jellyfish. In this study, we focus on phylogenetic analysis of the gene BracB, a member of the Brachyury subfamily in the moon jellyfish Aurelia coerulia, and use in situ hybridization to examine its expression pattern in the medusa formation process called strobilation. During strobilation, polyps undergo body “segmentation”, and each segment generates a single juvenile medusa. Our phylogenetic analysis suggests a duplication of Brachyury before the hydrozoa-scyphozoa divergence and groups the Aurelia Bracb with other medusozoan Bra2 genes. However, a second copy of Brachyury is not found in anthozoans or staurozoans. Our preliminary in situ hybridization suggests that BracB expression is endodermal in late strobila. We also find that BracB expression is in stripes concentrated towards the younger segments of the strobila. Our data provides the first expression profile of Brachyury in medusa formation, shedding some light on the role of Brachyury in medusa body plan patterning.