This study investigated the genetic structure of a population of the highly outcrossed perennial shrub, Banksia spinulosa. Three variable loci were detected; Pgm1, Adh1 and Pgi2, Some genetic differentiation was detected in the population, and as a whole it deviated from a panmictic unit. This primarily resulted from the behaviour of Pgi2. This locus exhibited a large deficit of heterozygotes, possibly in association with a Wahlund effect. However, deviations from panmixia were small compared with species which are predominantly self-fertilizing, and estimates of gene flow indicated that the movement of genes occurs over a fairly wide area. This study provides the first description of spatial genetic variability within a population of Banksia spinulosa.