ABSTRACT The unique morphology of quillworts has received limited attention, and such studies have been limited to only a few species. Our extensive field work during the past two decades has revealed variation in the structures of the plant, including the rhizomorph, scales, phyllopodia, and abscission caps. Polarity of the axes of southeastern quillwort rhizomorphs varies from discoid (most species), to elongate, to upright with axis branching in several species. In species of intermittent streams, these branched rhizomorphs produce plantlets that break off in running water. Scales are tiny brown or black structures in alternating whorls with sporophylls (leaves). They are often overlooked and easily removed when rinsing specimens. Found in most southeastern terrestrial/amphibious species, scales are absent from aquatic species. Scales are distinct from phyllopodia, the sclerified bases of sporophylls, but intermediates between scales and phyllopodia occur. Not all species with scales have phyllopodia. Although scales cannot be used for determination of species, their presence or absence is of taxonomic value. Research on southeastern Isoetes phylogeny could help determine which of the rhizomorph and scale characters are plesiomorphic.