Proper growth and patterning of tissues and organs require tight control of intercellular signaling which is assured by the existence of different feedback regulatory mechanisms. We are interested in identifying the impact of feedback regulators in BMP morphogen signaling and their influence on the establishment and maintenance of graded signaling. In Drosophila BMP morphogen signaling one regulatory feedback loop involves the BMP receptor Thickveins (Tkv). In the wing imaginal disc, BMP dependent transcriptional repression of tkv keeps the level of the receptor low near the source of the BMP ligand Decapentaplegic (Dpp). This allows efficient spreading of the ligand and the formation of a long range Dpp gradient. In contrast, in the haltere precursor, the evolutionary homologue of the wing, the Hox gene Ubx disables BMP from repressing tkv and high receptor levels trap the ligand and restraint its spreading. The resulting short-range Dpp gradient has been suggested to contribute to the smaller size of the haltere. We will report on the molecular circuit implementing differential tkv regulation. In particular, we will show how BMP target genes, previously assigned as effectors of the pathway, interact with Ubx and with cis–elements on tkv regulatory modules to differentially affect tkv transcription in the wing and haltere precursors. Based on our cis-analysis we use genome editing approaches to actively reshape tkv expression, the shape of the Dpp gradient and final organ size in vivo. Our results provide insights on the mechanisms by which evolution rewires regulatory feedback circuitry to produce signaling gradients of new shapes and, consequently, organs of different size and ultimately new function.