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Pilot Knob NWR was established in 1987. The 90-acre Refuge, a donation of the Pilot Knob Ore Company, is located on top of Pilot Knob Mountain in Iron County, Missouri. The Refuge contains abandoned iron mine shafts excavated in the mid-1800s that have since become critical habitat for the federally-listed endangered Indiana bat.
The Indiana bat hibernates within the abandoned mine shafts located at the peak of Pilot Knob Mountain. There are differing estimates of Pilot Knob NWR's Indiana bat population, but the number is likely within the range of 50,000 to 1000,000. The bats generally arrive in September and leave in April. To avoid disturbance to the bats, the Refuge is closed to all entry. The Refuge is managed by Mingo National Wildlife Refuge.