NUP98-HOXA9 induces leukemia-like phenotypes in Drosophila. The MEIS ortholog HTH collaborates with NUP98-HOXA9 in the fly hematopoietic system. NUP98-HOXA9 interferes with PVR signaling during lymph gland development. NUP98-HOXA9 reveals novel functional interactions between lymph gland compartments.