Abstract• The Spanish fir (Abies pinsapo Boiss.) is a conifer endemic to southern Spain and belongs to a Mediterranean basin group of firs considered to be relict. Megagametophyte storage proteins are a useful tool for the evaluation of genetic variability due to the haploid nature of megagametophytes in conifers.• In this paper, we report for the first time, the usefulness of megagametophyte storage proteins marker in A. pinsapo as a first investigation of the level of genetic diversity conserved in the extant stands of this relict conifer. For this, four populations were analysed from the three areas in which the species is still found. A total of thirty trees and ten megagametophytes per tree were analysed. In addition, 191 megagametophytes from two trees were assessed to identify polymorphic bands and to confirm Mendelian inheritance 1:1.• Albumins have proved to be a good marker to assess the genetic variability in this species, due to their high level of variation. Fourteen polymorphic bands adjusted to the expected 1:1 segregation ratio, two cases of allelism and eight of linkage were detected.• The genetic diversity study showed that, in the four populations, approximately half of the genetic diversity was among trees and the other half among seeds of each tree. Differentiation between populations was less than 6.0%. Results from this study could be useful for determining appropriate conservation management strategies for this endangered species.