Seed heteromorphism is the formation of different seed morphs from the same individual. Two seed morphs have been preliminarily observed in Leptocereus scopulophilus. One morph shows an apparent natural scarification of its coat. Herein we describe the seeds, taking into account shape, coat integrity, surface, dimensions, mass and the position of germination cracks. We defined two seed morphs using the integrity of the spermoderma: fragmented seed coats (FSC) and complete seed coats (CSC). We also evaluated minimum germination time, germination rate and germinability. The seed morphs did not differ significantly in traits; however, regular striations along the cuticle of the periclinal walls were more visible in the FSC compared with the CSC. Both seed morphs displayed anticlinal cell boundaries in the border region that are channelled and straight in the dorsal-ventral region but difficult to define in the lateral region. We found four morphological variations in different positions where the radicle or cotyledons emerge and variations in cuticle thickness in different regions of the seed that could determine the formation of cracks during germination. All germination variants occurred in both seed morphs, albeit in different proportions. Germination was higher and faster for the FSC compared with the CSC. These germination differences could be related to a thinner cuticle in the FSC and the punctual release of its spermoderma, which facilitates a quick imbibition of the embryo and the breaking of the seed coat. Our results indicate that differences in germination parameters between the two seed morphs relate to differences in the percentage of dormant seeds, which favour the temporal expansion of germination and reduce competition between siblings. To propagate the species for conservation purposes, we recommend using FSC, while CSC may be used to establish a seed collection ex situ.