A new species, Isoetes libanotica Musselman, Bolin & R. D. Bray (Isoetaceae, Lycophyta), is described from Akkar District of northern Lebanon. It is a seasonal terrestrial species of basaltic soils, diploid (2n = 22), with complete velum coverage. Megaspore diameter ranges from 338 to 477 μm with remote, low tuberculate ornamentation and a low to obsolete equatorial girdle; microspore length ranges from 25 to 30 μm, with echinate ornamentation. At the type locality of I. libanotica, two other Isoetes L. species occur sympatrically. These superficially similar Isoetes species can be differentiated from I. libanotica using megaspore characters; I. duriei Bory has larger alveolate megaspores and I. olympica A. Braun has a prominent equatorial girdle.