Recent molecular analyses demonstrate that Botrychium lunaria does not occur in North America except in Greenland, even in a restricted sense, following the description of B. neolunaria. The appropriate name for the remaining continental North American element of the Botrychium lunaria complex is Botrychium onondagense. Because B. neolunaria and B. onondagense are cryptic with respect to each other, we provide a morphological analysis comparing B. onondagense to B. neolunaria, a key, an illustration, and a map based on molecularly identified specimens.