ABSTRACT By genetically characterizing adult individuals, we documented the presumed prefragmentation population structure of an endangered Andean tree, Magnolia espinalii . Our sample included all known surviving individuals for this species. Genetic diversity was high, but genetic distance was not related to geographic distance between sites. Magnolia espinalii apparently was originally distributed in numerous semi‐isolated demes. The lack of evidence of recruitment around most adults in this species suggests a fragmentation‐related disruption of their reproductive ecology. Artificial propagation projects should obviously attempt to involve all 23 known surviving trees.