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The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P-p) and Shannon’s index (I), increased slightly within the seed bank over time, while gene diversity (H-j), did not change. P-p, I, and H-j all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H-j or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.