Conservation of rare species and ecosystem biodiversity should not lead to conflicts. However, situations may arise when the management of focal species places non-target species at risk. In the Willamette Valley of western Oregon, USA, eradication of a naturally hybridizing Grindelia integrifolia × Grindelia nana (Asteraceae) population from a wildlife refuge to preserve genetically “pure” populations of endemic G. integrifolia populations to the North, eliminated a dominant, late-summer, flowering plant from the plant community. While this decision undoubtedly arose from good intentions, the hybrid Grindelia was the sole pollen resource for the last known population (numbered in 100s prior to Grindelia removal) of an endemic solitary bee, Melissodes pullatella (Anthophoridae), a rare wetland butterfly, Lycaena xanthoides (Lycaenidae), and very likely additional pollinators. Approximately 15 years after the removal of Grindelia from the wildlife refuge, we found several small populations of M. pullatella (<20 individuals sighted) about 70 km to the south of the refuge in hybrid Grindelia-dominated remnant and restored wetlands. We present this case study to highlight the loss of local biodiversity that can accompany single species driven ecosystem management. We hope that land managers will consider not only the preservation of the formally recognized rare species in their conservation strategy but also the impacts of management practices on site biodiversity.