Isoetes melanopoda, a diploid species of ephemeral prairie wetland swales primarily in central North America, has also been found in swamp forests over a wide area of eastern North America in recent years. Determination of certain morphological and ecological characteristics (leaf width, habitat preference, leaf base color, megaspore ornamentation pattern, and megaspore size) distinguishes two population groupings within the species range that maintain discreet geographic distributions and thus represent distinct taxa. Most populations of these two eastern and western taxa are distinctive enough to argue for identification as separate species within I. melanopoda (s.l.). The existence of some apparently intermediate populations within a transition zone between the two taxa and the absence of stand-alone diagnostic identification features, however, indicates that a subspecific level of distinction is more appropriate. Isoetes melanopoda subsp. silvatica, subsp. nov., is proposed for the previously unnamed eastern taxon.