Sexual propagation of Agave plants is an incipient cultivation method, these plants withstand drought and adverse growing conditions; therefore, research on Agave’s diversity, seed processing, and storage could support its cultivation on marginal lands. The aim of this work was to evaluate seed morphology, germination, and seedling genetic diversity of six seed origins (species × provenance) of Agave plants collected in five provenances from Mexico. Seed longevity was evaluated in two seed origins after a 10-year storage period. Seed morphology and seedling genetic variation results demonstrated intra- and interspecific variation within Agave salmiana and with the other seed origins, respectively. After a 10-year storage period seed germination of two A. salmiana seed origins remained relatively stable, storage conditions, and seed variables of this work can serve as reference parameters for future analyses. To the best authors’ knowledge, this is the first report of Agave’s seed longevity evaluation after a 10-year storage period.