The scientific name of the Montana Arctic grayling, when treated as a subspecies, is Thymallus arcticus montanus. It was first described in 1874 as Thymallus montanus by fisheries biologist James W. Milner. The type specimen was collected by Acting Assistant Surgeon, George Scott Oximixon, U.S. Army near Camp Baker, Montana Territory. Camp Baker was located very close to the Smith river northwest of White Sulphur Springs in Meagher County. Milner also based his description on three specimens taken by geologist Ferdinand V. Hayden during his Geological Survey of 1872 from Willow Creek in Gallatin County, Montana.