The Banskia subgenus Isostylis complex is comprised of two rare and restricted species, B. cuneata and B. oligantha, and the widespread B. ilicifolia. Population genetic structure and genetic diversity were examined within and among the three species using 10 allozyme loci across 21 populations. Levels of genetic diversity did not appear to correspond with either population size or geographic distribution. The restricted species B. cuneata exhibited the highest levels of gene diversity (H es , 0.13) followed by the widespread B. ilicifolia (H es , 0.10) and the other restricted species B. oligantha (H es , 0.08). Similarly, there was no relationship between genetic structure and geographical distribution with the rare B. cuneata being highly structured (θ =0.370) compared with B. ilicifolia (θ =0.164) and B. oligantha (θ =0.221). The relatively low but similar levels of diversity present in the subgenus concur with those observed in other proteaceous genera and probably reflect historical events rather than a genetic effects associated with a recently fragmented landscape.