Cell identity and proliferation differs between organs, raising the question of how cells at interorgan boundaries are regulated to maintain organ integrity. On p. 4091, Don Fox and colleagues identify a specialised transition zone at the midgut/hindgut boundary in the Drosophila intestine. This ‘hybrid zone’, which shows gene expression profiles from both organs, changes in size during development but is maintained into adult life, and cells within it contribute to both midgut and hindgut tissue. The authors describe a new population of stem cells – the organ-boundary intestinal stem cells (OB-ISCs) – that reside in the midgut immediately adjacent to the hybrid zone and show slower division rates. Injury to the hybrid zone increases proliferation of these OB-ISCs, and if the injury is severe enough, hyperplastic OB-ISCs can cross the boundary and invade the hindgut. The authors find that OB-ISC proliferation is induced by release of the JAK-STAT ligand Unpaired-3 from the hindgut and the hybrid zone following injury. The hybrid zone therefore serves as a focal point of interorgan interaction to influence the behaviour of OB-ISCs and preserve the midgut/hindgut distinction, raising the possibility that interorgan regulation of stem cell behaviour may be a common mechanism to maintain organ identity.