In southern New South Wales, a suite of widespread plant species exhibit short-statured 'dwarf' growth forms on coastal headlands. It is unclear whether such populations are genetically distinct or whether dwarfism is a plastic response to the environment. We used four microsatellite markers to assess genetic differentiation among populations from coastal and inland sites for Banksia spinulosa var. spinulosa. We sampled plants from six locations, including from three 'dwarf' and three 'normal' populations. Mean levels of genetic diversity were slightly higher in the forest (N(a) = 7.07 +/- 0.25; H(e) = 0.80 +/- 0.09) than on the coast (N(a) = 5.92 +/- 0.70; H(e) = 0.72 +/- 0.10). In general, populations displayed genotypic diversity expected for outcrossed sexual reproduction, with 161 of 172 individuals displaying unique genotypes and mean values of F(IS) close to zero. However, we found evidence of at least limited clonal replication in each of four populations and, within one coastal population, 11 of 27 individuals displayed one of three replicated genotypes, implying that the effective population size may be considerably smaller than would be inferred from the number of plants at this site. Relative to studies with other Proteaceae, this set of populations showed low, although significant, levels of differentiation (global F(ST) = 0.061; P <0.001), with extremely low, although significant, divergence of forest and coastal populations (F(RT) = 0.009; P <0.001). There was no evidence of isolation by distance. These data imply that coastal dwarf populations are genetically similar to more extensive inland populations but in at least one case, may be at a greater risk of extinction because of low effective population size.