Hymenaea courbaril is an endangered species, promising to reforestation programs and mainly explored as a wood source. The available information concerning long-term storage methods, seed recalcitrance, parental, and substrate influence is scarce. This study focused on the seed behavior according to population origin and during one-year storage, also testing the efficiency of the low-temperature conservation. Variations between the uncertainty indexes were found to the studied populations after long-term storage. There was no significant loss of the germination potential in consequence of the prolonged storage period. Although, older seeds promoted gradually greater delayed germination. Germination speed, synchrony, and uncertainty indexes were substantially different between the -20° conservation and control. H. courbaril seeds are capable of long-term storage without losing their germination potential, indicating an orthodox behavior.