Conservation of global biodiversity requires studies of rare taxa at high risk for extinction due to anthropogenic impacts. Rhodiola integrifolia subsp. leedyi (Leedy's roseroot, Crassulaceae) is a rare cliff-dwelling subspecies federally listed as threatened in the United States. Thought to be glacial relicts, all seven known populations of Leedy's roseroot are endemic to cliffs, likely in large part due to the specific environmental factors at these cliffs. This study took place at Glenora Cliffs, New York, the location of the largest population of this subspecies in the world. We identified habitat factors associated with Leedy's roseroot occurrence by comparing areas where Leedy's roseroot was present to adjacent areas where Leedy's roseroot was absent. Leedy's roseroot occurrence was associated with increased light, lower height on the cliff, geologic features of the cliff including greater degree of water seeping from crevices, higher plant species richness, and higher mean temperatures, with temperature trends varying over the growing season. Leedy's roseroot stem length was correlated with decreased light and temperature, and cliff features. Analysis of the Glenora Cliffs plant species community suggested seepage and cliff features structure the community. Leedy's roseroot co-occurred with other cliff-dwelling species that may serve as indicators of Leedy's roseroot habitat. Our characterization of habitat factors associated with Leedy's roseroot supports its glacial relict status, suggests global climate change may impact it differently than most plant species, and informs management and potential ex situ conservation of this rare subspecies.