Colonial hydrozoans represent some of the most diverse and complex body plans within the Metazoa. Complex hydrozoans colonies are more physiologically and structurally integrated than their simple colonial relatives. Colonial integration is commonly associated with the regulation of the general structural plan of the colony, the division of labor, and the physiological integration of the colony. In the hydrozoan Hydractinia, these features are manifested through evolutionary innovations involving the spatial regulation of polyps within the colony, the development of polyp polymorphs, and the acquisition of a stolonal mat. These innovations all involve evolutionary changes in the regulation of polyp and colony-wide patterning systems. In Hydractinia, the ParaHox gene, Cnox-2, is expressed in a spatially restricted manner along the axes of stolons and polyps, suggesting that changes in the regulation of this gene may be in part responsible for the evolutionary innovations important for colonial complexity.