Hydration memory is a phenomenon in which a seed can tolerate discontinuous hydration periods, displaying enhanced germination after one or multiple hydration–dehydration (HD) cycles; it was described physiologically in a few cactus species around 15 years ago. Although no additional work was done on this subject, it has great biotechnological potential since its analysis would permit predictions about whether a seed can withstand discontinuous hydration; in the long run, the knowledge about its regulation might lead to induction of this resistance, so we aimed to provide an initial approach to the molecular mechanisms that underlie hydration memory. This phenomenon was reproduced successfully in our lab with Ferocactus peninsulae seeds. Using two-dimensional (2D) electrophoresis, we compared expression patterns of proteins involved in seed maturation of seeds and seedlings subjected to an HD cycle treatment. We found differential expression of several proteins possibly involved in primary metabolism, ubiquitination pathway and reserve protein availability regulation in seeds and seedlings subjected to an HD cycle. We also found differential stability of total RNA. These results strongly suggest that the differential expression of proteins is at least partially related to the hydration memory process.