Agave is one of the most important genera of plants in Mexico in terms of biodiversity and cultural and economic impact; however, its reproductive traits and breeding systems are poorly known. In addition, clonal propagation of agave cultures and the interruption of sexual reproduction may lead to differences not only in reproductive traits but also in seed set and seed viability across species and between wild plants and Agave landraces. Hence this research evaluated the morphological variation of flowers, fruits, and seeds throughout the infructescence development of pulquero agave landraces (Agave americana, A. mapisaga, and A. salmiana) and their wild relatives (A. salmiana) using statistical analyses. Additionally, seed set and seed viability (tetrazolium test) were estimated for traditional (metepantle) and intensive (monoculture) cultivation systems. The analysis of flowers allowed differentiating between species (A. mapisaga and A. salmiana), while the analysis of fruits separated wild from cultivated plants. Wild agaves attained seed set values close to 0.5, and cultivated agaves, less than 0.2; the lowest seed set values (0.04) were observed under monoculture. Seed viability percentages depended on the taxon analyzed, with no clear differences between wild and cultivated taxa. There were positive correlations between branch length, fruit number, black (potentially viable) seed number, and the percentage of viable seeds. The highest percentage of viable seeds was recorded in the low and middle parts of the infructescence. Our results demonstrate that reproductive traits are suitable for recognizing morphological groups across species and between wild and landrace agaves. They also show that intensive and prolonged clonal propagation is associated with low seed set and seed viability values in Agave landraces.