This thesis has focused on the evolutionary history of Isoetes (Isoetales, Lycopsida), its phylogeny, megaspore morphology and evolutionary path through deep time. With a broadened sampling of species to include more of the worldwide diversity of the genus compared to previous work an unexpected sister to the rest of the genus was found. Isoetes wormaldii Sim is a critically endangered species from the southeastern Cape region in South Africa, which grows in ponds and slow-moving streams. There are only a few, small populations, and they are very sensitive to habitat changes. The rest of Isoetes is divided into five major clades, which show complex and not readily understandable biogeographic patterns, and by which processes the species came to live in their current locations in the world is often a conundrum. The age of the extant Isoetes is intriguing as it could potentially explain some of the baffling geographic distributions. Analyses based on whole chloroplast genomes and nuclear cistrons found that the choice of clock model and which genome dataset the dating analysis is based on matter greatly when trying to date the genus as the results were highly inconsistent. The solution to the dating analysis woes might be dependent on finding new bases, e.g., fossil evidence, for age calibrations which would require the morphology of Isoetes to be better understood. Our study of megaspore morphology found substantial differences among species of Isoetes in both ornamentation and surface texture/structure. While no major clade within the genus could be unambiguously defined by their spore morphology there are some characteristics of smaller clades and patterns of ornamentation and surface texture across the phylogeny. Our tentative hypothesis is that a pustulate megaspore ornamentation and a cobwebby texture are ancestral features in the megaspore of Isoetes.