Botrychium spathulatum is similar to B. lunaria and B. minganense. All three are small (mostly less than 10 cm tall) and the veins of the pinnae radiate out in a fan-like pattern and lack a clear midrib. The pinnae of B. spathulatum tend to be less broadly fan-shaped than B. lunaria, and the fertile branch of B. spathulatum tends to be more extensively divided than that of B. minganense. Some plants of all three species can be very difficult to place. See steps 22-23 in the associated key, or refer to the Flora of North America treatment of Botrychium for further assistance.

Botrychium spathulatum has a very limited distribution, being known from scattered localities across Canada and extending only into a few sites in the United States in Montana, Michigan and Wisconsin. It's range appears to fall entirely within that of B. minganense, which it closely resembles. It is known from only one site in Wisconsin, and has been listed as a "special concern" species. Habitat appears to be mostly grassy, sunny sites.