In the conservation of endangered species, active suppression of a population of one native species to benefit another native species poses particular challenges. Obvious examples include predator control and nest parasite reduction. Less obvious is the control of blood-feeding arthropods. We present a case study on the effect of blood-feeding black flies (Simulium spp.) on reintroduced Whooping Cranes (Grus americana). Our intent is to provide a transferrable, science-driven approach for determining the effects of blood-feeding arthropods on endangered vertebrates, and demonstrate an approach for guiding selection of management actions for managers faced with competing objectives. A multi-year experiment demonstrated that black flies reduce nest success in reintroduced cranes by driving the birds off their nests during incubation. Deciding how to respond, however, is complicated because the target black flies are native species that serve important ecological functions. We suggest that a decision-analytic approach can inspire the development of creative management alternatives and facilitate a transparent process that evaluates trade-offs among competing objectives. Recognizing that these decisions involve trade-offs, which must be weighed in the context of each case, is crucial to identifying alternatives that best balance multiple management objectives. Given the uncertainty about the population dynamics of blood-feeding arthropods, an adaptive management approach will offer substantial benefits.