Huperzia appalachiana lacks annual constrictions on the stems and the gemmiferous branchlets may extend throughout the stem, in contrast to the similar H. selago that produces a single whorl ("pseudowhorl") near the end of each year's growth.

Huperzia appalachiana is known to occur at only a few sites in Wisconsin, near Lake Superior in Bayfield County. It is found mostly north of Wisconsin, around the north shore of Lake Superior, from New England north to Newfoundland and Labrador, and in the mountains from northern Georgia to Virginia. The Flora of North America describes the habitat as cliffs, rocks or talus.