Hematophagous insects can negatively affect the reproductive success of their vertebrate hosts. To determine the influence of hematophagous insects on endangered vertebrates requires specially designed programs that minimize disturbance to the hosts and address problems associated with their small populations. We developed and evaluated a surveillance program for black flies potentially affecting a population of whooping cranes (Grus americana) introduced to central Wisconsin, U.S.A. In one of the few studies to survey host-seeking female black flies and their immature stages concurrently, we processed nearly 346,000 specimens and documented 26 species, of which only two, Simulium annulus and Simulium johannseni, were attracted to nesting whooping cranes. Attempts to assess black fly populations with artificial nests and real crane eggs were unsuccessful. Carbon-dioxide traps performed well in describing black fly taxa on the landscape. However, the number of black flies at whooping crane nests was consistently higher than the number captured in carbon-dioxide traps. The carbon-dioxide traps poorly described the presence/absence, population fluctuations, and periodicity of black flies at whooping crane nests. The weak performance of the carbon-dioxide traps might have resulted from microhabitat differences between trap locations and nests or from Simulium annulus and Simulium johannseni using sensory cues in addition to carbon dioxide to find hosts. Choice of trapping techniques, therefore, depends on the information required for the particular study objectives.