One of the challenges when working with the genus Isoëtes is the scarcity of in-depth comparative analyses of its morphological characters. This paucity of analyses relates in part to the long-held conclusion that most of the characteristics associated with the traits of the genus aside from spore morphology, are too variable to be informative. As a result, our understanding of morphological variability among species of Isoëtes is underdeveloped. Recent workers have attempted to address this deficiency by examining the glossopodia of the ligule, a structure unique among living taxa to Isoëtes and its sister genus, Selaginella. The glossopodium is embedded in the adaxial surface of the microphyll, and has shown evidence of interspecific variability in the few studies in which it has been examined. However, these prior works were limited to qualitative comparisons. The present study compares 3D reconstructions of the glossopodia of three species, Isoëtes howellii, I. bolanderi and I. nuttallii, using morphometric analyses in addition to more traditional qualitative comparisons. MANOVA of measurements obtained from 3D reconstructions of the glossopodia show significant differences in size while elliptical Fourier analysis of these reconstructions demonstrates differences in shape among the species. These analyses provide a repeatable, statistical framework for future work on the glossopodium and potentially other traits in Isoëtes.