The Isoëtes karstenii complex includes those species characterized by laevigate megaspores, acute to free ala apices, a highly reduced labium, and distributions in the high altitude páramos of Venezuela, Colombia, and Ecuador. These species have been variously treated in the literature. Many early authors placed all Andean laevigate-spored specimens in Isoëtes lechleri, a central Andean species, while one later author recognized up to eight northern Andean species distinct from I. lechleri. This research represents a revisionary study to determine the number and identity of the taxa in this complex. Multivariate and descriptive analyses of morphological data and chromosome counts were performed. Five species are recognized including the previously described I. karstenii and I. palmeri. One variety is transferred from I. lechleri to I. karstenii (I. karstenii var. anomala). Three of the recognized species are newly described: I. fuliginosa, I. hemivelata and I. precocia. Chromosome counts revealed that I. karstenii and I. precocia are diploids (2n = 22) and that I. palmeri is tetraploid (2n = 44). Estimates of chromosome number based on spore size for I. fuliginosa and I. hemivelata indicate that they are polyploid (2n ≥ 44).