The distinguishing features of a previously unknown amphibious Isoetes discovered in coastal British Columbia, Canada are described. Although occurring in an ephemeral, vernal, seaside rock pool habitat thought to be indicative of I. nuttallii, field observations and morphological investigations determined these plants to be a distinctive taxon possessing small and boldly ornamented megaspores, relatively large microspores, and a regionally unique short velum coverage of the sporangia. It is reminiscent, particularly in spore ornamentation, of the aquatic, mid-season I. maritima and is known from one site (possibly two) where no living plants are presently evident. A unique combination of uncommon morphological features, restricted geographic range, rare habitat, and early growth season distinguishes these plants as distinct from all known Isoetes taxa. Isoetes salishensis, sp. nov. is proposed as an addition to the growing list of flora and fauna endemic to or centered on the Salish Sea area of southwestern British Columbia and northwestern Washington State.