Isoetes philippinensis, a critically endangered site-endemic lycophyte, was rediscovered after the last collection in 1969. The present study elucidates the morphology and ecology of the species – which have not been fully investigated – by describing the detailed morpho-anatomical characters, collecting water samples for physico-chemical analysis, and providing an in situ description of its habitat. The diagnostic characteristics of the species included long microphylls (up to 63 cm long), cobwebby megaspores and microspores, and the presence of velum. The morphology of I. philippinensis exhibits the features of other aquatic, amphibious and terrestrial species of Isoetes – such as the presence of lacuna in the roots, air chambers in the leaves, reduced stele, and abundance of parenchyma cells throughout the organs. Water-quality values are within the minimum acceptable limit. Threats to the population of I. philippinensis are discussed and characterized as Critically Endangered (CR A1c, B2a). The information presented here is vital for both in situ and ex situ conservation of the species.